A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 

A

abortTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Request that the ObjectStore aborts and closes the transaction, delegate to internal ObjectStoreWriter.
abortTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Request that the ObjectStoreWriter aborts and closes the transaction
abortTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter
Request that the ObjectStoreWriter aborts and closes the transaction
abortTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Aborts a transaction.
AbstractConstraint - Class in org.intermine.sql.query
An abstract representation of an item that can be present in the WHERE or HAVING sections of an SQL query.
AbstractConstraint() - Constructor for class org.intermine.sql.query.AbstractConstraint
 
AbstractHelper - Class in org.intermine.api.query.range
A class that can be extended to easily create RangeHelpers for a particular type.
AbstractHelper() - Constructor for class org.intermine.api.query.range.AbstractHelper
 
AbstractListService - Class in org.intermine.webservice.server.lists
Base class for list services.
AbstractListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.AbstractListService
 
AbstractQueryService<T> - Class in org.intermine.webservice.client.services
Common behaviour for services requesting results from a web-service.
AbstractQueryService(String, String, String) - Constructor for class org.intermine.webservice.client.services.AbstractQueryService
Constructor.
AbstractQueryService - Class in org.intermine.webservice.server.query
A base class for query services.
AbstractQueryService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.AbstractQueryService
Constructor.
AbstractRegionExportService - Class in org.intermine.bio.webservice
Base class for Biological region export services.
AbstractRegionExportService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.AbstractRegionExportService
Constructor.
AbstractTable - Class in org.intermine.sql.query
An abstract representation of an item that can be present in the FROM section of an SQL query.
AbstractTable() - Constructor for class org.intermine.sql.query.AbstractTable
 
AbstractTracker - Class in org.intermine.api.tracker
Abstract interface for creating trackers objects.
AbstractTracker(Queue<Track>, String) - Constructor for class org.intermine.api.tracker.AbstractTracker
Construct a Tracker setting the tracks queue and the table name
AbstractValue - Class in org.intermine.sql.query
An abstract representation of an item that can be present in the SELECT, GROUP BY, or ORDER BY sections of an SQL query, as well as in a constraint.
AbstractValue() - Constructor for class org.intermine.sql.query.AbstractValue
 
accept(EitherVisitor<A, B, T>) - Method in class org.intermine.webservice.server.core.Either
How you go about accessing the values.
accept(EitherVisitor<A, B, T>) - Method in class org.intermine.webservice.server.core.Either.Left
 
accept(EitherVisitor<A, B, T>) - Method in class org.intermine.webservice.server.core.Either.Right
 
AcceptanceTestTask - Class in org.intermine.task
A Task to run acceptance tests, configurable from a file.
AcceptanceTestTask() - Constructor for class org.intermine.task.AcceptanceTestTask
 
acceptInvitation(SharingInvite, Profile) - Method in class org.intermine.api.bag.SharedBagManager
Accept this invitation.
act(Emailer) - Method in interface org.intermine.web.context.MailAction
Inject an emailer, and do something.
action - Variable in class org.intermine.api.search.TaggingEvent
 
Action - Class in org.intermine.task.project
Base class for actions in a project.xml files
Action() - Constructor for class org.intermine.task.project.Action
 
add(Map<String, String>) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ExpressionList
Put/add to the list
add(Map<String, String>) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ExpressionList
Put/add to the list
add(Map<String, String>) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList
Put/add to the map of expressions
add(Integer) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList.StainingLevel
 
ADD - Static variable in class org.intermine.objectstore.query.QueryExpression
Addition of two numeric fields
add(Query) - Method in class org.intermine.sql.precompute.BestQuery
Allows a Query to be added to this tracker.
add(String) - Method in class org.intermine.sql.precompute.BestQuery
Allows a Query to be added to this tracker.
add(Query) - Method in class org.intermine.sql.precompute.BestQueryExplainer
Allows a Query to be added to this tracker.
add(String) - Method in class org.intermine.sql.precompute.BestQueryExplainer
Allows a Query to be added to this tracker.
add(BestQueryExplainer.Candidate) - Method in class org.intermine.sql.precompute.BestQueryExplainer
Allows a Candidate to be added to this tracker.
add(Query) - Method in class org.intermine.sql.precompute.BestQueryFallback
Allows a Query to be added to this tracker.
add(String) - Method in class org.intermine.sql.precompute.BestQueryFallback
Allows a Query to be added to this tracker.
add(Query) - Method in class org.intermine.sql.precompute.BestQueryLogger
Allows a Query to be added to this tracker.
add(String) - Method in class org.intermine.sql.precompute.BestQueryLogger
Allows a Query to be added to this tracker.
add(Query) - Method in class org.intermine.sql.precompute.BestQueryStorer
Allows a Query to be added to this tracker.
add(String) - Method in class org.intermine.sql.precompute.BestQueryStorer
Allows a Query to be added to this tracker.
add(Query) - Method in class org.intermine.sql.precompute.EncloseSubqueryBestQuery
Allows a Query to be added to this tracker.
add(String) - Method in class org.intermine.sql.precompute.EncloseSubqueryBestQuery
Allows a Query to be added to this tracker.
add(PrecomputedTable) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Add a precomputed table to the underlying database.
add(PrecomputedTable, Collection<String>) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Add a precomputed table to the underlying database.
add(AbstractConstraint) - Method in class org.intermine.sql.query.ConstraintSet
Add an AbstractConstraint to this ConstraintSet.
add(AbstractValue) - Method in class org.intermine.sql.query.Function
Adds an operand to this Function object.
add(Constant) - Method in class org.intermine.sql.query.InListConstraint
Add constants to the list.
add(E) - Method in class org.intermine.util.ConsistentSet
Add an object to the set.
add(Integer) - Method in class org.intermine.util.IntPresentSet
Adds an int to the set.
add(E) - Method in class org.intermine.util.PseudoSet
add(Object) - Method in class org.intermine.web.logic.results.InlineResultsTableRow
Add an InlineTableResultElement or an empty String
add(Item) - Method in class org.intermine.webservice.client.lists.ItemList
 
add(Object) - Method in class org.intermine.webservice.client.results.ResultRowList
 
add(int, Object) - Method in class org.intermine.webservice.client.results.ResultRowList
 
add(Map.Entry<K, V>, boolean) - Method in interface org.intermine.webservice.server.jbrowse.MapListener
 
add(Map<K, V>, boolean) - Method in interface org.intermine.webservice.server.jbrowse.MapListener
 
ADD_HEADER_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
The parameter for requesting column headers
addAccession(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
addAll(Collection<? extends Constant>) - Method in class org.intermine.sql.query.InListConstraint
Adds a Collection of Constants to the list.
addAll(Collection<? extends E>) - Method in class org.intermine.util.ConsistentSet
Add a whole Collection of objects to the set.
addAll(Collection<? extends E>) - Method in class org.intermine.util.PseudoSet
addAll(Collection) - Method in class org.intermine.webservice.client.lists.ItemList
 
addAll(Collection<? extends Object>) - Method in class org.intermine.webservice.client.results.ResultRowList
 
addAll(int, Collection<? extends Object>) - Method in class org.intermine.webservice.client.results.ResultRowList
 
addAllToBag(ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Adds a collection of elements to an ObjectStoreBag, delegate to internal ObjectStoreWriter.
addAllToBag(ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Adds a collection of elements to an ObjectStoreBag.
addAllToBag(ObjectStoreBag, Collection<Integer>) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Adds a collection of elements to an ObjectStoreBag.
addAllToBagWithConnection(Connection, ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Adds elements to the given bag.
addAnchor(String) - Method in class org.intermine.web.struts.ForwardParameters
Add an anchor to the path.
addAndConstraint(Query, Constraint) - Static method in class org.intermine.objectstore.query.QueryHelper
Add a constraint to be ANDed with those present in a Query.
addAspectSource(AspectSource) - Method in class org.intermine.web.logic.aspects.Aspect
Add a AspectSource.
addAttribute(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
holds the value until the item is processed/stored on the next line
addAttribute(Attribute) - Method in class org.intermine.xml.full.Item
Add an attribute.
addBag(ObjectStoreBag) - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
Adds a bag to this combination
addBagCombination(ObjectStoreBagCombination) - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
 
addBagDisplayer(Displayer) - Method in class org.intermine.web.logic.config.Type
Add a bag displayer for this Type
addBagValues() - Method in class org.intermine.api.profile.InterMineBag
Save the key field values associated to the bag into bagvalues table
addBagValues(Collection<BagValue>) - Method in class org.intermine.api.profile.StorableBag
Save the values given in input into bagvalues table
addBatches - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
addByChadoId(Integer, ChadoCVTerm) - Method in class org.intermine.bio.chado.ChadoCV
Add a cvterm and its chado id to this cv.
addCacheLine(String, String, int) - Method in class org.intermine.sql.precompute.OptimiserCache
Adds a new OptimiserCacheLine object to the cache.
addCanonicalIsoform(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
sets isIsoform to be false.
addChild(LogicExpression.Node) - Method in class org.intermine.pathquery.LogicExpression.And
Adds a node to the collection of children.
addChild(LogicExpression.Node) - Method in class org.intermine.pathquery.LogicExpression.Operator
Adds a node to the collection of children.
addChild(LogicExpression.Node) - Method in class org.intermine.pathquery.LogicExpression.Or
Adds a node to the collection of children.
addClass(LuceneObjectClass) - Method in class org.intermine.web.autocompletion.LuceneIndex
added a new LuceneObjectClass to internal map
addCollection(ReferenceList) - Method in class org.intermine.xml.full.Item
Add a collection.
addCollectionCount(String, String, Object, String) - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary
Add collection count to the summary.
addCollectionDistinctCount(String, String, Object, String) - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary
Add collection distinct count to the summary.
addCollectionElement(Object, String, Object) - Static method in class org.intermine.metadata.TypeUtil
Adds an element to a public or protected collection of an Object given the field name.
addCollectionToCurrentNode(Path) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Adds a new list, representing a collection to the current node (map)
addColumn(Database, String, String, DatabaseUtil.Type) - Static method in class org.intermine.sql.DatabaseUtil
Add a column in the table specified in input.
addColumn(Connection, String, String, DatabaseUtil.Type) - Static method in class org.intermine.sql.DatabaseUtil
Add a column to an existing database table, if it does not already exist.
AddColumnAction - Class in org.intermine.web.struts
AddColumnAction adds new column to existing WebTable that should be displayed.
AddColumnAction() - Constructor for class org.intermine.web.struts.AddColumnAction
 
addColumns(List<Path>) - Method in class org.intermine.api.results.WebResults
 
addColumns(List<Path>) - Method in interface org.intermine.api.results.WebTable
Adds columns that should be displayed to the table.
addCommentRefId(String, Integer) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
addComponent(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
addConstraint(Constraint) - Method in class org.intermine.objectstore.query.ConstraintSet
Add a Constraint to the set
addConstraint(PathConstraint) - Method in class org.intermine.pathquery.PathQuery
Adds a PathConstraint to this query.
addConstraint(PathConstraint, String) - Method in class org.intermine.pathquery.PathQuery
Adds a PathConstraints to this query, associated with a given constraint code.
addConstraints(Collection<PathConstraint>) - Method in class org.intermine.pathquery.PathQuery
Adds a collection of constraints to this query.
addConstraints(PathConstraint...) - Method in class org.intermine.pathquery.PathQuery
Adds a group of constraints to this query.
addCustom(String, String, Object, String, String) - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary
Add a custom object to the displayer.
addCVTermColon(String) - Static method in class org.intermine.bio.dataconversion.FlyBaseProcessor
For a FlyBase cvterm identifier like "FBbt00000001", add a colon in the middle and return: "FBbt:00000001"
addDataSet(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Add an DataSet Item to this handler, to be retrieved later with getDataSetReferenceList().
addDbref(String, String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
add dbref to list.
addEarlyItem(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Add a new Item to the Collection returned by getItems, at the beginning.
addECNumber(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
addElement(StringBuilder, String, String) - Method in class org.intermine.webservice.server.output.XMLFormatter
Add an element with some content.
addEntry(String, String, String, Collection<String>, Boolean) - Method in class org.intermine.bio.dataconversion.IdResolver
Add an entry to the IdResolver, a primary identifier and any number of synonyms.
addEvidence(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry.Comment
Will be replaced later with publication
addExecution(TemplateTrack) - Method in class org.intermine.api.tracker.TemplatesExecutionMap
Add a new template track into the map
addFeature(Item) - Method in class org.intermine.bio.dataconversion.UniprotEntry
new feature for protein feature.type and feature.description are set first.
addFeatureLocation(String, String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
addField(String) - Method in class org.intermine.web.autocompletion.LuceneObjectClass
addField added field to the class
addFieldConfig(FieldConfig) - Method in class org.intermine.web.logic.config.Type
Add a FieldConfig for this Type
addFieldToMap(ResultElement, Path, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Adds the attributes contained in the cell to the map given.
addFileSet(FileSet) - Method in class org.intermine.bio.dataconversion.UniprotFilterTask
Set the source fileset.
addFileSet(FileSet) - Method in class org.intermine.bio.task.GFF3ConverterTask
Set the data fileset
addFileSet(FileSet) - Method in class org.intermine.dataloader.XmlDataLoaderTask
Set the data fileset
addFileSet(FileSet) - Method in class org.intermine.task.FileConverterTask
Set the data fileset
addFileSet(FileSet) - Method in class org.intermine.task.FileDirectDataLoaderTask
Add a FileSet to read from.
addFileSet(FileSet) - Method in class org.intermine.task.FullXmlConverterTask
Set the data fileset
addFrom(FromElement) - Method in interface org.intermine.objectstore.query.HasFromList
Adds a FromElement to the FROM clause of this Query
addFrom(FromElement) - Method in class org.intermine.objectstore.query.Query
Adds a FromElement to the FROM clause of this Query
addFrom(FromElement, String) - Method in class org.intermine.objectstore.query.Query
Adds a FromElement to the FROM clause of this Query
addFrom(FromElement) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Adds an element to the FROM list.
addFrom(FromElement, String) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Adds an element to the FROM list, including an alias.
addFrom(AbstractTable) - Method in class org.intermine.sql.query.Query
Adds a table to the from list of this query.
addGeneDesignation(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
geneDesignation is required in the case of a single protein having multiple gene identifiers.
addGeneName(String, String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
From
addGlobalRepository() - Method in class org.intermine.api.search.SearchRepository
Add a global repository
addGOEvidence(String, String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
addGOTerm(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
addGroupBy(AbstractValue) - Method in class org.intermine.sql.query.Query
Adds a field to the GROUP BY clause of this query.
addHaving(AbstractConstraint) - Method in class org.intermine.sql.query.Query
Adds a constraint to the HAVING clause of this query.
addHeaderConfigLink(HeaderConfigLink) - Method in class org.intermine.web.logic.config.Type
Add a header configuration, used from WebConfig
addHeaderConfigTitle(HeaderConfigTitle) - Method in class org.intermine.web.logic.config.Type
Add a header configuration, used from WebConfig
addIdentifier(String, String, String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
example: 6239.primaryIdentifier.dbref = WormBase 6239.secondaryIdentifier.name = ORF [taxonId].
addIdsFromResultSet(ResultSet, OrganismRepository, String) - Method in class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory
Add results from query to ID resolver
addIdsFromResultSet(ResultSet) - Method in class org.intermine.bio.dataconversion.OntologyIdResolverFactory
Add results from query to ID resolver
addIdsToBag(Collection<Integer>, String) - Method in class org.intermine.api.profile.InterMineBag
Add the given ids to the bag, this updates the bag contents in the database.
addIdsToList(Collection<? extends String>, InterMineBag, String, String, Set<String>, Collection<String>) - Method in class org.intermine.webservice.server.lists.ListUploadService
Adds objects to the a bag for the matches against a set of identifiers.
addIdToBag(Integer, String) - Method in class org.intermine.api.profile.InterMineBag
Add the given id to the bag, this updates the bag contents in the database. he type can be a qualified or un-qualified class name.
addImageLink(String, String, String, String) - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary
Add a link to an image for the summary.
addIndex(String, String, Connection) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Adds an index to the given table on the given field.
addInlineList(InlineListConfig) - Method in class org.intermine.web.logic.config.Type
Add an InlineList for this object, used from WebConfig
addIsoform(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
addIsoformSynonym(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
if an isoform has two ID tags, then the first one is used and the second one is added as a synonym
addIssue(String, String, String, List) - Method in class org.intermine.api.bag.BagQueryResult
Add an issue to this result.
addItem(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Add a new Item to the Collection returned by getItems().
AdditionalConverter - Class in org.intermine.api.bag
Represents an additional converter config
AdditionalConverter(String, String, String, String, String) - Constructor for class org.intermine.api.bag.AdditionalConverter
Create a new AdditionalConverter object.
additionsFiles - Variable in class org.intermine.task.ModelMergerTask
 
addJsonProperty(StringBuffer, String, Object) - Method in class org.intermine.pathquery.PathQuery
Add a JSON property when serialising
addKey(Map<String, List<FieldDescriptor>>, String, FieldDescriptor) - Static method in class org.intermine.api.config.ClassKeyHelper
Add a key to set of keys for a given class.
addKeyword(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
addLinkedFeature(String, DefaultModelledFeature) - Method in class org.intermine.webservice.server.complexes.ExportService.FeatureHolder
 
addListener(MapListener<String, Object>) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
addLongDisplayer(Displayer) - Method in class org.intermine.web.logic.config.Type
Add a long displayer for this Type
addMainIds(String, String, String, Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver
Add alternative main identifiers for a primary identifier to the IdResolver.
addMainIds(String, String, Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver
Add alternative main identifiers for a primary identifier to the IdResolver.
addMatch(String, Integer) - Method in class org.intermine.api.bag.BagQueryResult
Add a new match from an input string to an InterMineObject id.
addModel(String, Model) - Static method in class org.intermine.metadata.Model
Adds model to known models.
addModel(Model) - Method in class org.intermine.pathquery.PathQueryHandler
 
addNonCoveredFrom(Set<T>, Set<T>, Set<T>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Adds all required FROM items to the FROM list of the new query.
addObserver(WebSearchWatcher) - Method in class org.intermine.api.profile.StorableBag
 
addObserver(WebSearchWatcher) - Method in interface org.intermine.api.search.WebSearchable
Add this observer to the list of interested parties.
addObserver(WebSearchWatcher) - Method in class org.intermine.api.template.ApiTemplate
 
addOrderBy(String, OrderDirection) - Method in class org.intermine.pathquery.PathQuery
Adds an element to the order by list of this query.
addOrderBy(OrderElement) - Method in class org.intermine.pathquery.PathQuery
Adds an element to the order by list of this query.
addOrderBy(AbstractValue) - Method in class org.intermine.sql.query.Query
Adds a field to the ORDER BY clause of this query.
addOrderBys(Collection<OrderElement>) - Method in class org.intermine.pathquery.PathQuery
Adds a group of elements to the order by list of this query.
addOrderBys(OrderElement...) - Method in class org.intermine.pathquery.PathQuery
Adds a group of elements to the order by list of this query.
addOrderBySpaceSeparated(String) - Method in class org.intermine.pathquery.PathQuery
Adds a group of elements to the order by list, given a space-separated list.
addOutputAttribute(String, String) - Method in class org.intermine.webservice.server.widget.WidgetService
Wrapper around addOutputInfo that makes sure we don't add empty values.
addOutputConfig(WidgetConfig) - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService
 
addOutputConfig(WidgetConfig) - Method in class org.intermine.webservice.server.widget.GraphService
 
addOutputConfig(WidgetConfig) - Method in class org.intermine.webservice.server.widget.TableWidgetService
 
addOutputConfig(WidgetConfig) - Method in class org.intermine.webservice.server.widget.WidgetService
Add metadata about the widget we are using.
addOutputFilter(WidgetConfig, String, InterMineBag) - Method in class org.intermine.webservice.server.widget.WidgetService
Add information about the filters as attributes to the result.
addOutputInfo(String, String) - Method in class org.intermine.webservice.server.core.JSONService
Add a key value pair to put in the header of json results.
addOutputListInfo(InterMineBag) - Method in class org.intermine.webservice.server.widget.WidgetService
Add metadata about the list we are processing.
addOutputResult(Widget) - Method in class org.intermine.webservice.server.widget.WidgetService
Send results to the outside world.
addParam(String, String) - Method in class org.intermine.web.logic.config.Displayer
Add a stored parameter to this Displayer.
addParameter(String, String) - Method in class org.intermine.web.struts.ForwardParameters
Add a parameter to the path.
addParameter(String, String) - Method in interface org.intermine.webservice.client.core.Request
Adds parameter.
addParameter(String, String) - Method in class org.intermine.webservice.client.core.RequestImpl
Adds parameter.
addParent(String) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
 
addPostProcess(String, PostProcess) - Method in class org.intermine.task.project.Project
Add a post-processing step
addProblem(String) - Method in class org.intermine.metadata.Model
Add a problem to the model that doesn't prevent it from being created for backwards compatibility but should be checked when creating a new model.
addProperty(UserProperty) - Method in class org.intermine.task.project.Project
Add a project property.
addProteinName(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
the name section in uniprot can contain several names, eg. recommendedName, alternateName, etc.
addPub(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
addPubEvidence(String, String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
addPublication(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Add an Publication Item to this handler, to be retrieved later with getPublicationReferenceList().
addRange(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
addReference(Query, QueryClass, String, String) - Method in class org.intermine.web.logic.widget.WidgetLdr
Add a contains constraint to Query (q) built with the query class and attribute given in input
addReference(Reference) - Method in class org.intermine.xml.full.Item
Add a reference.
addReferenceConstraint(Model, Query, QueryClass, String, QueryClass, boolean) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil
Add a contains constraint to Query (q) from qcStart from qcEnd via reference refName.
addReferencedCellToJsonMap(ResultElement, Path, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Adds the information from a cell representing a reference to the map given.
addReferenceToCurrentNode(Path) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Adds an intermediate reference to the current node.
addRefId(String) - Method in class org.intermine.xml.full.ReferenceList
Add a value to the list of references.
addReportDisplayer(ReportDisplayerConfig) - Method in class org.intermine.web.logic.config.WebConfig
Add config for a report page displayer.
addRequest(ResultsBatches, int, boolean, boolean) - Static method in class org.intermine.objectstore.query.PrefetchManager
Adds a request to the Set of pending requests, and wakes up a Thread to handle it.
addResolverEntry(String, String, String, Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver
Create entries for the IdResolver, these will be added when getIdResolver is called.
addResolverEntry(String, String, Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver
Create entries for the IdResolver, these will be added when getIdResolver is called.
addResultElementToTableRow(Object, Object) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable
Add a result element (RE or "" String)
addResultElementToTableRow(Object, Object) - Method in class org.intermine.web.logic.results.InlineResultsTable
Add a result element (RE or "" String), used for type safety as overriden on BagUploadConfirm
addResultEntries(Collection<Map.Entry<String, Object>>) - Method in class org.intermine.webservice.server.core.JSONService
 
addResultEntries(Collection<Map.Entry<String, Object>>, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a bunch of entries.
addResultEntry(String, Object, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a single entry.
addResultEntry(Map.Entry<String, Object>, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a single entry.
addResultItem(Map<String, ? extends Object>, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a map of names and values as a JSON object.
addResultItem(List<? extends Object>, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a list of objects as a JSON array.
addResultItem(List<String>) - Method in class org.intermine.webservice.server.output.MemoryOutput
Add result item to memory.
addResultItem(List<String>) - Method in class org.intermine.webservice.server.output.Output
Adds data to output.
addResultItem(List<String>) - Method in class org.intermine.webservice.server.output.StreamedOutput
Forwards data to associated writer
addResultValue(CharSequence, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a char-sequence as a JSON value.
addResultValue(Number, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a number as a JSON value.
addResultValue(Boolean, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a bool as a JSON value.
addRole(String) - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
Add a role to this permission.
addRow(String...) - Method in class org.intermine.metadata.TextTable
Adds a single row to the table.
addRow(Connection, String, Object, String[], Object[]) - Method in class org.intermine.sql.writebatch.Batch
Adds a row to the batch for a given table.
addRow(Connection, String, String, String, int, int) - Method in class org.intermine.sql.writebatch.Batch
Adds a row to the batch for a given indirection table.
addRow(int, int) - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Adds a row to the batch.
addRow(Object, String[], Object[]) - Method in class org.intermine.sql.writebatch.TableBatch
Adds a row to the batch.
addSelect(SelectValue) - Method in class org.intermine.sql.query.Query
Adds a field to the select list of this query.
addSelectedToBag(InterMineBag) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Adds the selected object ids to the given bag.
addSource(String, Source) - Method in class org.intermine.task.project.Project
Add a Source object
addSubtab(String, String) - Method in class org.intermine.web.logic.results.WebState
Set the subtab for a particular tab
addSummaryConstraint(SummaryConstraint) - Method in class org.intermine.web.logic.querybuilder.SummaryPath
Add a constraint to that applies to this path.
addSynonym(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Keep track of the synonyms per line.
addSynonym(OboTermSynonym) - Method in class org.intermine.bio.ontology.OboTerm
Add a synonym for this term.
addSynonyms(List<String>) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Keep track of the synonyms per line.
addSynonyms(String, String, String, Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver
Add synonyms for a primary identifier to the IdResolver
addSynonyms(String, String, Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver
Add synonyms for a primary identifier to the IdResolver
addSynonyms(OboTerm, List<?>, String) - Method in class org.intermine.bio.ontology.OboParser
Add synonyms to a DagTerm.
addTableExportConfig(TableExportConfig) - Method in class org.intermine.web.logic.config.WebConfig
Add an TableExportConfig to the Map of TableExportConfig objects using tableExportConfig.getId() as the Map key.
addTableToDatabase(PrecomputedTable, Collection<String>, boolean) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Add a PrecomputedTable to the database.
addTag(String, String, String, Profile) - Method in class org.intermine.api.profile.TagManager
Add a new tag.
addTag(String, WebSearchable, Profile) - Method in class org.intermine.api.profile.TagManager
Associate a websearchable obj with a certain tag.
addTag(String, ClassDescriptor, Profile) - Method in class org.intermine.api.profile.TagManager
Associate a class with a certain tag.
addTag(String, ReferenceDescriptor, Profile) - Method in class org.intermine.api.profile.TagManager
Associate a reference with a certain tag.
addTag(String, String, String) - Static method in class org.intermine.dwr.AjaxServices
Adds tag and assures that there is only one tag for this combination of tag name, tagged Object and type.
addTag(String) - Method in class org.intermine.webservice.client.services.ListService.ListOperationInfo
Add a tag to the set of tags to apply.
addTags(String...) - Method in class org.intermine.webservice.client.lists.ItemList
Add some new tags to this list.
addTags(ItemList, String...) - Method in class org.intermine.webservice.client.services.ListService
Get the tags for a list after adding some to the tag set.
addTags(Collection<? extends String>) - Method in class org.intermine.webservice.client.services.ListService.ListOperationInfo
Add some tags to the set of tags to apply.
addTagsToBag(Collection<String>, InterMineBag, Profile) - Method in class org.intermine.api.bag.BagManager
Add tags to a bag.
addTime(long) - Method in class org.intermine.objectstore.intermine.ExtraQueryTime
Adds statistics for an executed query to this object.
addTitleParts(HashMap<String, List<HeaderConfigTitle.TitlePart>>) - Method in class org.intermine.web.logic.config.HeaderConfigTitle
Add title parts to this header config.
addToBag(ObjectStoreBag, Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Adds an element to an ObjectStoreBag, delegate to internal ObjectStoreWriter.
addToBag(ObjectStoreBag, Integer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Adds an element to an ObjectStoreBag.
addToBag(ObjectStoreBag, Integer) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Adds an element to an ObjectStoreBag.
AddToBagAction - Class in org.intermine.web.struts
Action to save a single object o an existing bag.
AddToBagAction() - Constructor for class org.intermine.web.struts.AddToBagAction
 
addToBagFromQuery(Query) - Method in class org.intermine.api.profile.InterMineBag
Add elements to the bag from a query, this is able to operate entirely in the database without needing to read objects into memory.
addToBagFromQuery(ObjectStoreBag, Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Adds elements to an ObjectStoreBag, delegate to internal ObjectStoreWriter.
addToBagFromQuery(ObjectStoreBag, Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Adds elements to an ObjectStoreBag from the results of a Query.
addToBagFromQuery(ObjectStoreBag, Query) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Adds elements to an ObjectStoreBag from the results of a Query.
addToBagFromQueryWithConnection(Connection, ObjectStoreBag, Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Adds elements to a bag from the results of a query.
addToCollection(Integer, Class<?>, String, Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Add an object to another object's collection, delegate to internal ObjectStoreWriter.
addToCollection(Integer, Class<?>, String, Integer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Place an object in a many-to-many collection of another object.
addToCollection(Integer, Class<?>, String, Integer) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Place an object in a many-to-many collection of another object.
addToCollection(String, Item) - Method in class org.intermine.xml.full.Item
Add the identifier of the given Item to a collection.
addToCollection(String, String) - Method in class org.intermine.xml.full.Item
Add a reference to a collection of this item.
addToCollectionWithConnection(Connection, Integer, Class<?>, String, Integer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Performs addToCollection with given connection
addToConstraintLogic(LogicExpression, String) - Static method in class org.intermine.api.query.MainHelper
Add a constraint code to a logic expression, ANDed with any constraints already in the expression, e.g.
addToFeatureMap(Integer, FeatureData) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Override method that adds completed features to featureMap.
addToFeatureMap(Integer, FeatureData) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Add feature data to FeatureMap, can be overidden by subclasses that need to store some features in additional maps.
addToFrom(String) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
addToGroupBy(QueryNode) - Method in class org.intermine.objectstore.query.Query
Add a QueryNode to the GROUP BY clause of this Query
addToHolder(Object) - Method in class org.intermine.util.CacheHoldingArrayList
Adds an object to the holder.
addToLastBatch(String) - Method in class org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl
Adds a statement to the lastBatch.
addToLastBatch(String) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Adds a statement to the lastBatch.
addToList(List<Constraint>, Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Adds all the constraints present in the argument into the given List.
addToListMap(Map<K, List<V>>, K, V) - Static method in class org.intermine.metadata.Util
Add a value to a Map from keys to Set of values, creating the value list as needed.
addToOrderBy(String) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
addToOrderBy(QueryOrderable) - Method in class org.intermine.objectstore.query.Query
Add a QueryOrderable to the ORDER BY clause of this Query
addToOrderBy(QueryOrderable, String) - Method in class org.intermine.objectstore.query.Query
Add a QueryOrderable to the ORDER BY clause of this Query
addToPostDeleteBatch(String) - Method in class org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl
Adds a statement to the postDeleteBatch.
addToPostDeleteBatch(String) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Adds a statement to the postDeleteBatch.
addToPreDeleteBatch(String) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Adds a statement to the preDeleteBatch.
addToSelect(QuerySelectable) - Method in class org.intermine.objectstore.query.Query
Add a QuerySelectable to the SELECT clause of this Query
addToSelect(QuerySelectable, String) - Method in class org.intermine.objectstore.query.Query
Add a QuerySelectable to the SELECT clause of this Query
addToSelect(QuerySelectable) - Method in interface org.intermine.objectstore.query.Queryable
Adds an element to the SELECT list.
addToSelect(QuerySelectable) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Adds an element to the SELECT list.
addToSelect(QuerySelectable) - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Adds an element to the SELECT list.
addToSelect(QuerySelectable) - Method in interface org.intermine.objectstore.query.QueryPathExpressionWithSelect
Adds an element to the SELECT list.
addToSetMap(Map<K, Set<V>>, K, Collection<V>) - Static method in class org.intermine.metadata.Util
Add values to a Map from keys to Set of values, creating the value list as needed.
addToSetMap(Map<K, Set<V>>, K, V) - Static method in class org.intermine.metadata.Util
Add a value to a Map from keys to Set of values, creating the value list as needed.
addToSortOrder(String, String) - Method in class org.intermine.dwr.AjaxServices
Add a Node from the sort order
addToUnion(Query) - Method in class org.intermine.sql.query.Query
Adds another Query to the UNION set of this query.
addToView(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Add a path to the results view.
addToWhere(String) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
addType(Type) - Method in class org.intermine.web.logic.config.WebConfig
Add a type to the WebConfig Map.
addUniqueItemId(String, String) - Method in class org.intermine.dataconversion.DataConverter
List of unique identifiers and their refIds.
addUnmatchedId(String) - Method in class org.intermine.webservice.client.lists.ItemList
Add a new unmatched id to the set of unmatched identifiers.
addUnmatchedIds(Collection<String>) - Method in class org.intermine.webservice.client.lists.ItemList
Add some new unmatched ids to the set of unmatched identifiers.
addUnresolved(Collection<String>) - Method in class org.intermine.api.bag.BagQueryResult
Set the Map of unresolved input strings.
addUserProperty(UserProperty) - Method in class org.intermine.task.project.Action
Add a UserProperty to the Action
addUserToShareBag(String, String) - Method in class org.intermine.dwr.AjaxServices
Share the bag given in input with the user which userName is input and send email
addValueToField(String, String) - Method in class org.intermine.web.autocompletion.LuceneObjectClass
addValueToField added a new value to one existing field
addView(String) - Method in class org.intermine.pathquery.PathQuery
Add a single element to the view list.
addViews(Collection<String>) - Method in class org.intermine.pathquery.PathQuery
Adds a group of elements to the view list.
addViews(String...) - Method in class org.intermine.pathquery.PathQuery
Adds a group of elements to the view list.
addViewSpaceSeparated(String) - Method in class org.intermine.pathquery.PathQuery
Adds a group of elements to the view list, given a space-separated list.
addWhere(AbstractConstraint) - Method in class org.intermine.sql.query.Query
Adds a constraint to the where clause for this query.
addWidget(WidgetConfig) - Method in class org.intermine.web.logic.config.Type
Add a widget to the Type
addWidget(WidgetConfig) - Method in class org.intermine.web.logic.config.WebConfig
 
addXref(OboTerm) - Method in class org.intermine.bio.ontology.OboTerm
Add a xref for this term.
addXrefs(OboTerm, List<?>) - Method in class org.intermine.bio.ontology.OboParser
Add xrefs to a DagTerm.
aDescendsFromB(String, String) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Test whether a class named "a" descends from a class named "b".
adjustPValues(ErrorCorrection.Strategy, Map<String, BigDecimal>, Double, int) - Static method in class org.intermine.web.logic.widget.ErrorCorrection
 
advance(int) - Method in class org.intermine.webservice.client.results.Page
Advance to a new page my a given number of steps.
af - Variable in class org.intermine.web.struts.ForwardParameters
Original ActionForward.
AgeGroupLdr - Class in org.intermine.model.testmodel.web.widget
 
AgeGroupLdr(InterMineBag, ObjectStore, String) - Constructor for class org.intermine.model.testmodel.web.widget.AgeGroupLdr
 
AgeSalaryLdr - Class in org.intermine.model.testmodel.web.widget
 
AgeSalaryLdr(InterMineBag, ObjectStore, String) - Constructor for class org.intermine.model.testmodel.web.widget.AgeSalaryLdr
 
AgeSeniorityLdr - Class in org.intermine.model.testmodel.web.widget
 
AgeSeniorityLdr(InterMineBag, ObjectStore, String) - Constructor for class org.intermine.model.testmodel.web.widget.AgeSeniorityLdr
 
aIsaB(String, String) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Test whether a class named "A" is, or descends from, a class named "B".
ajaxCollapse(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
AJAX request - collapse a model browser node.
ajaxEditConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
AJAX request - edit an existing constraint.
ajaxEditJoinStyle(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Edit a constraint's join style settings for a path, and forward to queryBuilderConstraint, for use by ajax.
ajaxEditTemplateConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
AJAX request - edit a template constraint.
ajaxExpand(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
AJAX request - expand a model browser node.
ajaxNewConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
AJAX request - ahow the panel for adding a new constraint to the query.
ajaxRenderPaths(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
AJAX request - render query paths.
AjaxServices - Class in org.intermine.dwr
This class contains the methods called through DWR Ajax
AjaxServices() - Constructor for class org.intermine.dwr.AjaxServices
 
ajaxShowDisplayer(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails
Show a displayer in response to an AJAX request.
ajaxTemplateCount(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails
Count number of results for a template for inline templates
ajaxVerbosify(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails
 
AKA - Static variable in class org.intermine.api.profile.UserPreferences
What we should call the user.
ALIAS - Static variable in class org.intermine.api.profile.UserPreferences
The alias of this user.
alias(String) - Method in class org.intermine.dataconversion.DataConverter
Uniquely alias a className
alias(Object, String) - Method in class org.intermine.objectstore.query.Query
Set an alias for an element in the Query.
alias - Variable in class org.intermine.sql.query.AbstractTable
 
alias - Variable in class org.intermine.sql.query.SelectValue
 
alias - Variable in class org.intermine.task.DropPrecomputedTablesTask
 
alias - Variable in class org.intermine.task.PrecomputeTask
 
alias - Variable in class org.intermine.task.RunIqlQueryTask
 
alias - Variable in class org.intermine.task.SummariseObjectStoreTask
 
alias - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
ALL - Static variable in class org.intermine.api.search.Scope
User or global scope for bags, templates, etc.
ALL_BAGS - Static variable in class org.intermine.api.search.SearchTarget
The search target for all bags
ALL_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint
 
ALL_TEMPLATES - Static variable in class org.intermine.api.search.SearchTarget
The search target for all templates
ALLBUTINTERSECT - Static variable in class org.intermine.objectstore.query.ObjectStoreBagCombination
Constant representing an all but intersect operation
allDigits(String) - Static method in class org.intermine.metadata.StringUtil
Return true if all characters in a given String are digits.
allPkClassesEmptyForClass - Variable in class org.intermine.dataloader.HintingFetcher
 
allSources - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
ALT_NAME_PARAM - Static variable in class org.intermine.webservice.server.lists.ListInput
The name of the new list (synonym)
alterComparisonAnd(int, int) - Static method in class org.intermine.sql.query.AbstractConstraint
Take a couple of integers as if they are values returned by compare, and assume that they are two loose (and possibly different) descriptions of the relation between the same two AbstractConstraints, and return a value that is a more strict description.
alterComparisonAORB(int, int) - Static method in class org.intermine.sql.query.AbstractConstraint
Take a couple of integers as if they are values returned by compare, for this compared to A, and this compared to B, and return the value that compare should return for this compared to (A OR B).
alterComparisonNotObj(int) - Static method in class org.intermine.sql.query.AbstractConstraint
Take an integer as if it is a value returned by compare, and return the value that compare would have returned if second constraint (obj) had been NOTed.
alterComparisonNotThis(int) - Static method in class org.intermine.sql.query.AbstractConstraint
Take an integer as if it is a value returned by compare, and return the value that compare would have returned if first constraint (this) had been NOTed.
alterComparisonSwitch(int) - Static method in class org.intermine.sql.query.AbstractConstraint
Take an integer as if it is a value returned by compare, and return the value that compare would have returned if this and obj had been switched.
ALWAYS_EXPLAIN_TABLES - Static variable in class org.intermine.sql.precompute.BestQueryExplainer
 
AlwaysMap<K,V> - Class in org.intermine.util
This is a dumb implementation of a Map.
AlwaysMap(V) - Constructor for class org.intermine.util.AlwaysMap
Construct an AlwaysMap.
AlwaysSet<E> - Class in org.intermine.util
A Set that always returns true for the contains method.
amendTo(String) - Method in class org.intermine.api.profile.InvalidBag
Fix this bag by changing its type.
analyse(Database, boolean) - Static method in class org.intermine.sql.DatabaseUtil
Analyse given database, perform vacuum full analyse if full parameter true.
analyse(Database, ClassDescriptor, boolean) - Static method in class org.intermine.sql.DatabaseUtil
Analyse database table for a given class and all associated indirection tables.
AnalyseDbTask - Class in org.intermine.task
Task to run ANALYSE on a table or whole database.
AnalyseDbTask() - Constructor for class org.intermine.task.AnalyseDbTask
 
anchor - Variable in class org.intermine.web.struts.ForwardParameters
Anchor name.
AND - Static variable in class org.intermine.metadata.ConstraintOp
Combine constraints with the AND operation
and(EitherVisitor<A, B, R>) - Method in class org.intermine.webservice.server.core.EitherVisitor
Compose this visitor with another visitor which handles the either after this one has had a go at it, presumably for side-effects like logging and what-not.
annotationClassName - Variable in class org.intermine.bio.dataconversion.GoConverter
 
AnonProfile - Class in org.intermine.api.util
A null-object for profiles for use with the web services.
AnonProfile() - Constructor for class org.intermine.api.util.AnonProfile
Constructor
API - Interface in org.intermine.api
The interface of the API, abstracted for testing purposes.
api - Variable in class org.intermine.webservice.server.core.WebServiceServlet
 
ApiJavaController - Class in org.intermine.web.struts
 
ApiJavaController() - Constructor for class org.intermine.web.struts.ApiJavaController
 
ApiPerlController - Class in org.intermine.web.struts
 
ApiPerlController() - Constructor for class org.intermine.web.struts.ApiPerlController
 
ApiTemplate - Class in org.intermine.api.template
This class extends TemplateQuery to provide the features needed by the API - Lucene indexing and database serialisation.
ApiTemplate(String, String, String, PathQuery) - Constructor for class org.intermine.api.template.ApiTemplate
 
ApiTemplate(TemplateQuery) - Constructor for class org.intermine.api.template.ApiTemplate
Construct a new API template that has all the same properties as the TemplateQuery passed into the constructor.
apiTemplateMapToJson(InterMineAPI, Map<String, ApiTemplate>) - Static method in class org.intermine.api.template.TemplateHelper
Helper routine for serialising a map of templates to JSON.
apiTemplateMapToXml(Map<String, ApiTemplate>, int) - Static method in class org.intermine.api.template.TemplateHelper
Serialse a map of templates to XML.
append(String) - Method in class org.intermine.model.StringConstructor
Appends a String onto the end of this object.
append(Object) - Method in class org.intermine.model.StringConstructor
Appends an Object onto the end of this object.
append(boolean) - Method in class org.intermine.model.StringConstructor
Appends a boolean onto the end of this object.
append(int) - Method in class org.intermine.model.StringConstructor
Appends an int onto the end of this object.
append(long) - Method in class org.intermine.model.StringConstructor
Appends a long onto the end of this object.
append(float) - Method in class org.intermine.model.StringConstructor
Appends a float onto the end of this object.
append(double) - Method in class org.intermine.model.StringConstructor
Appends a double onto the end of this object.
append(String) - Method in class org.intermine.pathquery.Path
Return new Path that has this Path as its prefix and has fieldName as the last element.
append(String...) - Method in class org.intermine.webservice.client.lists.ItemList
Add new items to the list by resolving the identifiers of objects.
append(Collection<? extends String>) - Method in class org.intermine.webservice.client.lists.ItemList
Add new items to the list by resolving the identifiers of objects.
append(Item...) - Method in class org.intermine.webservice.client.lists.ItemList
Add new items to the list.
append(PathQuery) - Method in class org.intermine.webservice.client.lists.ItemList
Add new items to the list by resolving the identifiers of objects.
append(ItemList, String...) - Method in class org.intermine.webservice.client.services.ListService
Append some objects corresponding to identifiers to the given list, returning a list representing the new state.
append(ItemList, Collection<? extends String>) - Method in class org.intermine.webservice.client.services.ListService
Append some objects corresponding to identifiers to the given list, returning a list representing the new state.
append(ItemList, PathQuery) - Method in class org.intermine.webservice.client.services.ListService
Append the objects contained in the result set of a given query to the given list, returning a list representing the new state.
APPLICATION_JSON - Static variable in class org.intermine.webservice.client.core.ContentType
A ContentType constant that describes the JSON content type.
APPLICATION_JSON_OBJ - Static variable in class org.intermine.webservice.client.core.ContentType
A Content type that describes the JSON objects content type.
APPLICATION_JSON_ROW - Static variable in class org.intermine.webservice.client.core.ContentType
A Content type that describes the JSON rows content type.
apply(Map<String, BigDecimal>, PopulationInfo, Map<String, PopulationInfo>, Double) - Method in class org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient
 
apply(Constraint) - Method in class org.intermine.objectstore.intermine.CheckForIsNotNullConstraint
Perform test for NOT NULL constraint on node
apply(Constraint) - Method in interface org.intermine.objectstore.query.ConstraintTraverseAction
The apply() method is called by ConstraintHelper.traverseConstraints() for each Constraint and sub-Constraint.
apply(Map<String, BigDecimal>, PopulationInfo, Map<String, PopulationInfo>, Double) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient
Apply the correction coefficient to the pValuesTerm given in input
ArrayFormatter - Class in org.intermine.webservice.server.jbrowse.util
Not good practice, but this is how JBrowse wants results, so when in Rome.
ArrayFormatter() - Constructor for class org.intermine.webservice.server.jbrowse.util.ArrayFormatter
 
asList() - Method in class org.intermine.api.search.SearchResult
A list of between two and three items containing the information in this result.
asList() - Method in interface org.intermine.objectstore.proxy.LazyCollection
Return this Collection as a List.
asList() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Return this Collection as a List.
asList() - Method in class org.intermine.objectstore.query.Results
Return this Collection as a List.
Aspect - Class in org.intermine.web.logic.aspects
Configuration for a single data set.
Aspect() - Constructor for class org.intermine.web.logic.aspects.Aspect
 
AspectBinding - Class in org.intermine.web.logic.aspects
Routines for unmarshaling Aspect objects from XML.
AspectController - Class in org.intermine.web.struts
Contoller for a single data set tile embedded in a page.
AspectController() - Constructor for class org.intermine.web.struts.AspectController
 
ASPECTS - Static variable in class org.intermine.web.logic.Constants
Servlet context attribute - map from aspect set name to Aspect object.
AspectSource - Class in org.intermine.web.logic.aspects
Describes a source of data contributing to some data set.
AspectSource() - Constructor for class org.intermine.web.logic.aspects.AspectSource
 
AspectTagUtil - Class in org.intermine.api.tag
Util class for working with aspect tags.
asSearchConstraint() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
 
assignMapping(Integer, Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Puts a mapping into idMap.
assureOutputFormatSpecified(Request) - Method in class org.intermine.webservice.client.core.Service
Add a format parameter to match the content-type if there is one.
assureSize(int) - Method in class org.intermine.util.SensibleByteArrayOutputStream
Resizes the buffer to ensure it is as large as newSize.
ASYMMETRIC_SUBTRACT - Static variable in class org.intermine.api.bag.BagOperations
Constant representing logical asymmetric substraction.
AsymmetricOperationInput - Class in org.intermine.webservice.server.lists
A list input class for operations that have a left and a right side.
AsymmetricOperationInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.AsymmetricOperationInput
Constructor.
asymmetricSubtract(Model, Collection<InterMineBag>, Collection<InterMineBag>, String, Profile, ClassKeys) - Static method in class org.intermine.api.bag.BagOperations
 
AT_LEAST - Static variable in class org.intermine.objectstore.query.ResultsInfo
Denotes that the known number of rows has a minimum which exceed the estimate.
AT_MOST - Static variable in class org.intermine.objectstore.query.ResultsInfo
Denotes that the known number of rows has a maximum, and the estimate exceeds it.
ATTR_MARKER_RE - Static variable in class org.intermine.api.LinkRedirectManager
 
Attribute - Class in org.intermine.xml.full
Representation of an Attribute in an object
Attribute() - Constructor for class org.intermine.xml.full.Attribute
Constructor
Attribute(String, String) - Constructor for class org.intermine.xml.full.Attribute
Construnctor
ATTRIBUTE_TYPES - Static variable in class org.intermine.pathquery.PathQueryHandler
This is a list of String type descriptions that are attribute types
AttributeDescriptor - Class in org.intermine.metadata
Describes an attribute of a class - i.e. a field that is neither an object reference or a collection.
AttributeDescriptor(String, String) - Constructor for class org.intermine.metadata.AttributeDescriptor
Construct, name and type cannot be null.
AttributeLinksController - Class in org.intermine.bio.web
Set up maps for attributeLinks.jsp
AttributeLinksController() - Constructor for class org.intermine.bio.web.AttributeLinksController
 
AttributeLinkURL - Class in org.intermine.web.util
Simple class that parses provided url.
AttributeLinkURL(String) - Constructor for class org.intermine.web.util.AttributeLinkURL
Constructor.
attributeOp - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
attributeOptions - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
attributes - Variable in class org.intermine.webservice.server.query.result.QueryResultService
 
attributeValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
AuthenticatedListService - Class in org.intermine.webservice.server.lists
A Class that insists on being authenticated.
AuthenticatedListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.AuthenticatedListService
Constructor.
Authenticator - Class in org.intermine.web.struts.oauth2
The action that bounces the user off to their respective authentication provider when they want to use them to log-in with OAuth2.
Authenticator() - Constructor for class org.intermine.web.struts.oauth2.Authenticator
 
AUTO_COMPLETER - Static variable in class org.intermine.web.logic.Constants
ServletContext attribute, autocompletion.
AUTOCOMPLETE_INDEX - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key to use to store the autocomplete RAMIndexes.
AutoCompleter - Class in org.intermine.web.autocompletion
Autocompleter class for initializing and using the autocompletion
AutoCompleter() - Constructor for class org.intermine.web.autocompletion.AutoCompleter
Autocompleter standard constructor.
AutoCompleter(ObjectStore, Properties) - Constructor for class org.intermine.web.autocompletion.AutoCompleter
Autocompleter build index constructor.
AutoCompleter(InputStream) - Constructor for class org.intermine.web.autocompletion.AutoCompleter
Autocompleter rebuild constructor.
AvailableColumnsController - Class in org.intermine.web.struts
Controller for availableColumns.tile.
AvailableColumnsController() - Constructor for class org.intermine.web.struts.AvailableColumnsController
 
AvailableListsService - Class in org.intermine.webservice.server.lists
A service to report what lists a user has access to, and some details of those lists.
AvailableListsService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.AvailableListsService
Constructor
AvailableListsServlet - Class in org.intermine.webservice.server.lists
 
AvailableListsServlet() - Constructor for class org.intermine.webservice.server.lists.AvailableListsServlet
 
AvailableServicesServlet - Class in org.intermine.webservice.server
Report whether a requested service is implementented on this mine.
AvailableServicesServlet() - Constructor for class org.intermine.webservice.server.AvailableServicesServlet
 
AvailableTemplatesService - Class in org.intermine.webservice.server.template
Fetch the names of public template queries for use with the Templates web service.
AvailableTemplatesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.AvailableTemplatesService
Constructor.
AvailableWidgetsService - Class in org.intermine.webservice.server.widget
A service for listing the available widgets.
AvailableWidgetsService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.AvailableWidgetsService
Constructor
AvailableWidgetsServlet - Class in org.intermine.webservice.server.widget
Servlet handling requests for information about which widgets are available.
AvailableWidgetsServlet() - Constructor for class org.intermine.webservice.server.widget.AvailableWidgetsServlet
 
AVERAGE - Static variable in class org.intermine.objectstore.query.QueryFunction
Average value of a number of rows
AVG - Static variable in class org.intermine.sql.query.Function
AVG(v) aggregate function - takes one operand.

B

backgroundFlush(Connection, Set<String>) - Method in class org.intermine.sql.writebatch.Batch
Flushes the batch out to the database server, but does not guarantee that the operation is finished when this method returns.
backgroundFlush(Connection, Set<String>, boolean) - Method in class org.intermine.sql.writebatch.Batch
Flushes the batch out to the database server, but does not guarantee that the operation is finished when this method returns.
BadQueryException - Exception in org.intermine.api.query
 
BadQueryException(String, Exception) - Constructor for exception org.intermine.api.query.BadQueryException
 
BadRequestException - Exception in org.intermine.webservice.client.exceptions
The BadRequestException is thrown by service when there is a problem with the request.
BadRequestException(String) - Constructor for exception org.intermine.webservice.client.exceptions.BadRequestException
 
BadRequestException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.BadRequestException
 
BadRequestException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.BadRequestException
 
BadRequestException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.BadRequestException
 
BadRequestException - Exception in org.intermine.webservice.server.exceptions
The BadRequestException is thrown by service when there is a problem with the request.
BadRequestException(String) - Constructor for exception org.intermine.webservice.server.exceptions.BadRequestException
400 - BAD REQUEST
BadRequestException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.BadRequestException
404 - BAD REQUEST
BadRequestException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.BadRequestException
404 - BAD REQUEST
BadTemplateException - Exception in org.intermine.api.profile
Exception thrown when template has invalid name.
BadTemplateException() - Constructor for exception org.intermine.api.profile.BadTemplateException
Constructor
BadTemplateException(String) - Constructor for exception org.intermine.api.profile.BadTemplateException
Constructor with message.
BAG - Static variable in class org.intermine.api.tag.TagTypes
Bag.
bag - Variable in class org.intermine.objectstore.query.BagConstraint
 
bag - Variable in class org.intermine.web.logic.widget.Widget
 
bag - Variable in class org.intermine.web.logic.widget.WidgetLdr
 
BAG_INVITES - Static variable in class org.intermine.api.bag.SharedBagManager
The name of the table to persist offers to share a bag with others.
BAG_NAME_PREFIX - Static variable in class org.intermine.web.logic.bag.BagHelper
When generating new bag names, this is used as a prefix.
BAG_QUERY_MAX_BATCH_SIZE - Static variable in class org.intermine.webservice.server.lists.ListUploadService
The maximum number of ids to query for each batch.
BAG_VALUES - Static variable in class org.intermine.api.profile.InterMineBag
name of bag values table
BagBuildController - Class in org.intermine.web.struts
Controller Action for buildBag.jsp
BagBuildController() - Constructor for class org.intermine.web.struts.BagBuildController
 
BagConstraint - Class in org.intermine.objectstore.query
Constrain a QueryClass or QueryEvaluable to be within a bag.
BagConstraint(QueryNode, ConstraintOp, Collection<?>) - Constructor for class org.intermine.objectstore.query.BagConstraint
Construct a BagConstraint from a Collection.
BagConstraint(QueryNode, ConstraintOp, ObjectStoreBag) - Constructor for class org.intermine.objectstore.query.BagConstraint
Construct a BagConstraint from an ObjectStoreBag.
bagConstraintTables - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
bagConstraintToString(SqlGenerator.State, StringBuffer, BagConstraint, Query, DatabaseSchema, int) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a BagConstraint object into a String suitable for putting on an SQL query.
BagConversionHelper - Class in org.intermine.web.logic.bag
Utility methods used when converting lists (bags) between types.
BagConverter - Class in org.intermine.web.logic.bag
 
BagConverter(InterMineAPI, WebConfig) - Constructor for class org.intermine.web.logic.bag.BagConverter
 
BagDetailsAction - Class in org.intermine.web.struts
Action that builds a PagedCollection to view a bag.
BagDetailsAction() - Constructor for class org.intermine.web.struts.BagDetailsAction
 
BagDetailsController - Class in org.intermine.web.struts
 
BagDetailsController() - Constructor for class org.intermine.web.struts.BagDetailsController
 
BagDoesNotExistException - Exception in org.intermine.api.profile
Exception thrown when bag is not found.
BagDoesNotExistException() - Constructor for exception org.intermine.api.profile.BagDoesNotExistException
Constructor
BagDoesNotExistException(String) - Constructor for exception org.intermine.api.profile.BagDoesNotExistException
Constructor with message.
BagDoesNotExistException(Throwable) - Constructor for exception org.intermine.api.profile.BagDoesNotExistException
Constructor with throwable
BagDoesNotExistException(String, Throwable) - Constructor for exception org.intermine.api.profile.BagDoesNotExistException
Constructor with message and throwable
BagHelper - Class in org.intermine.web.logic.bag
Helper methods for bags.
BAGID_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the bagid column in the osbag table.
BagManager - Class in org.intermine.api.bag
A BagManager provides access to all global and/or user bags and methods to fetch them by type, etc.
BagManager(Profile, Model) - Constructor for class org.intermine.api.bag.BagManager
The BagManager references the super user profile to fetch global bags.
bagManager - Variable in class org.intermine.api.InterMineAPI
 
bagManager - Variable in class org.intermine.api.query.QueryExecutor
 
bagManager - Variable in class org.intermine.webservice.server.core.JSONService
 
bagManager - Variable in class org.intermine.webservice.server.lists.ListInput
 
bagManager - Variable in class org.intermine.webservice.server.query.QueryToListService
 
BagManager.ByTagOrder - Class in org.intermine.api.bag
Compare lists based on their im:order:n tag
BagManager.ByTagOrder() - Constructor for class org.intermine.api.bag.BagManager.ByTagOrder
 
BagManager.CaseInsensitiveComparator - Class in org.intermine.api.bag
Lower-case key comparator
BagManager.CaseInsensitiveComparator() - Constructor for class org.intermine.api.bag.BagManager.CaseInsensitiveComparator
 
bagName - Variable in class org.intermine.web.struts.ModifyBagDetailsForm
 
bagName - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
BagNotFound - Exception in org.intermine.api.query
 
BagNotFound(String) - Constructor for exception org.intermine.api.query.BagNotFound
 
BagNotFound(String, Throwable) - Constructor for exception org.intermine.api.query.BagNotFound
 
bagOp - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
BagOperation - Class in org.intermine.api.bag.operations
 
BagOperation(Model, Profile, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.BagOperation
 
BagOperationException - Exception in org.intermine.api.bag.operations
 
BagOperationException() - Constructor for exception org.intermine.api.bag.operations.BagOperationException
Constructor
BagOperationException(String) - Constructor for exception org.intermine.api.bag.operations.BagOperationException
 
BagOperationException(Throwable) - Constructor for exception org.intermine.api.bag.operations.BagOperationException
 
BagOperationException(String, Throwable) - Constructor for exception org.intermine.api.bag.operations.BagOperationException
 
BagOperations - Class in org.intermine.api.bag
Perform logical operations on bags - combine bags to create new InterMineBags
BagProducer - Interface in org.intermine.api.bag.operations
Functional interface for BagOperations, so we can be all forward looking.
BagQuery - Class in org.intermine.api.bag
A class encapsulating a query used to create a bag from a collection of input identifiers.
BagQuery(BagQueryConfig, Model, String, String, String, boolean) - Constructor for class org.intermine.api.bag.BagQuery
Create a new BagQuery object.
BagQuery(BagQueryConfig, Model, Map<String, List<FieldDescriptor>>, String) - Constructor for class org.intermine.api.bag.BagQuery
Create a new BagQuery object for the default query - search for all key fields of the given class.
BagQueryConfig - Class in org.intermine.api.bag
Configuration for BagQuery objects.
BagQueryConfig(Map<String, List<BagQuery>>, Map<String, List<BagQuery>>, Map<String, Set<AdditionalConverter>>) - Constructor for class org.intermine.api.bag.BagQueryConfig
Create a new BagQueryConfig object.
bagQueryConfig - Variable in class org.intermine.api.InterMineAPI
 
BagQueryHandler - Class in org.intermine.api.bag
Handler for bag-query.xml files.
BagQueryHandler(Model) - Constructor for class org.intermine.api.bag.BagQueryHandler
Create a new BagQueryHandler object.
BagQueryHelper - Class in org.intermine.api.bag
 
BagQueryResult - Class in org.intermine.api.bag
Class to hold the results of querying for a bag of objects.
BagQueryResult() - Constructor for class org.intermine.api.bag.BagQueryResult
 
BagQueryResult.IssueResult - Class in org.intermine.api.bag
Simple struct to hold three pieces of information together.
BagQueryResult.IssueResult(String, String, List) - Constructor for class org.intermine.api.bag.BagQueryResult.IssueResult
 
BagQueryRunner - Class in org.intermine.api.bag
For a given list of input strings search for objects using default and configured queries for a particular type.
BagQueryRunner(ObjectStore, Map<String, List<FieldDescriptor>>, BagQueryConfig, TemplateManager) - Constructor for class org.intermine.api.bag.BagQueryRunner
Construct with configured bag queries and a map of type -> key fields.
bagQueryRunner - Variable in class org.intermine.api.InterMineAPI
 
bagQueryRunner - Variable in class org.intermine.api.query.QueryExecutor
 
BagQueryUpgrade - Class in org.intermine.api.bag
 
BagQueryUpgrade(BagQueryRunner, InterMineBag) - Constructor for class org.intermine.api.bag.BagQueryUpgrade
 
BagResultCategoryKeyFormatter - Class in org.intermine.webservice.server.idresolution
Format a bag query result, grouping by category of issue.
BagResultCategoryKeyFormatter(InterMineAPI) - Constructor for class org.intermine.webservice.server.idresolution.BagResultCategoryKeyFormatter
 
BagResultFormatter - Interface in org.intermine.webservice.server.idresolution
 
BagResultOutputKeyFormatter - Class in org.intermine.webservice.server.idresolution
Format a bag result grouping by matched object.
BagResultOutputKeyFormatter(InterMineAPI) - Constructor for class org.intermine.webservice.server.idresolution.BagResultOutputKeyFormatter
 
BagSet - Class in org.intermine.api.profile
A class containing valiud and invalid bags.
BagSet(Map<String, InterMineBag>, Map<String, InvalidBag>) - Constructor for class org.intermine.api.profile.BagSet
Constructor
BagState - Enum in org.intermine.api.profile
Enumeration for describing the state of a bag: current not current (= the upgrading process has not been executed yet) upgrading (= the upgrading process is upgrading it) to upgrade (= the upgrading process has not been able to upgrade it because there are some conflicts that the user has to solve manually ))
bagTablesInDatabase - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
bagTablesToRemove - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
BagUpgradeAction - Class in org.intermine.web.struts
An action that prepare a BagQueryResult and save it into the session.
BagUpgradeAction() - Constructor for class org.intermine.web.struts.BagUpgradeAction
 
BagUploadConfirmAction - Class in org.intermine.web.struts
Action class for saving a bag from the bagUploadConfirm page into the user profile.
BagUploadConfirmAction() - Constructor for class org.intermine.web.struts.BagUploadConfirmAction
 
BagUploadConfirmController - Class in org.intermine.web.struts
Controller for the bagUploadConfirm; retrieve an IDResolutionService job id
BagUploadConfirmController() - Constructor for class org.intermine.web.struts.BagUploadConfirmController
 
BagUploadConfirmForm - Class in org.intermine.web.struts
Form for the bagUploadConfirm page.
BagUploadConfirmForm() - Constructor for class org.intermine.web.struts.BagUploadConfirmForm
Constructor
BagUploadConfirmInlineResultsTable - Class in org.intermine.web.logic.results
An inline table of ResultElements used ob BagUploadConfirm At the moment, we use this custom class to create a custom type of table row that will be extended with identifier and rowspan attributes needed on list upload confirmation step
BagUploadConfirmInlineResultsTable(Collection<?>, Model, WebConfig, Map<String, List<FieldDescriptor>>, int, boolean, List<Class<?>>) - Constructor for class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable
Construct a new InlineResultsTable object
BagUploadConfirmInlineResultsTableRow - Class in org.intermine.web.logic.results
Used on BagUploadConfirmIssueController (List upload confirm step) to add an identifier the user was trying to resolve with the number of rows in the ResultsTable corresponding to the said identifier.
BagUploadConfirmInlineResultsTableRow() - Constructor for class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
 
BagUploadConfirmIssueController - Class in org.intermine.web.struts
Controller for the bagUploadConfirmIssue tile.
BagUploadConfirmIssueController() - Constructor for class org.intermine.web.struts.BagUploadConfirmIssueController
 
BAGVAL_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the value column in the osbag table.
BagValue - Class in org.intermine.api.profile
A class representing a value stored in an InterMineBag.
BagValue(String, String) - Constructor for class org.intermine.api.profile.BagValue
Constructor
bagValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
Base64PublicKeyDecoder - Class in org.intermine.web.security
A public key decoder that reads public keys encoded as base64 strings.
Base64PublicKeyDecoder() - Constructor for class org.intermine.web.security.Base64PublicKeyDecoder
Construct a new decoder.
BaseDisclosureTag - Class in org.intermine.web.tags.disclosure
Base tag handler from which are all disclosure tag handlers derived.
BaseDisclosureTag() - Constructor for class org.intermine.web.tags.disclosure.BaseDisclosureTag
 
BaseEquivalentObjectFetcher - Class in org.intermine.dataloader
Class providing methods to look up equivalent objects by primary key in a production objectstore.
BaseEquivalentObjectFetcher(Model, IntToIntMap, ObjectStore) - Constructor for class org.intermine.dataloader.BaseEquivalentObjectFetcher
Constructor for this EquivalentObjectFetcher.
BASIC_FORMATS - Static variable in enum org.intermine.webservice.server.Format
The basic formats: HTML, TEXT, XML, JSON
batch - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
Batch - Class in org.intermine.sql.writebatch
A class representing a collection of writes to an SQL database.
Batch(BatchWriter) - Constructor for class org.intermine.sql.writebatch.Batch
Constructs an empty Batch, with no tables.
BATCH_SIZE - Static variable in class org.intermine.api.config.Constants
Batch size for the underlying objectstore
BATCH_SIZE - Static variable in class org.intermine.bio.dataconversion.EntrezOrganismRetriever
 
BATCH_SIZE - Static variable in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
 
BATCH_SIZE - Static variable in class org.intermine.webservice.server.query.result.QueryResultService
Batch size to use
batchCommit(Connection) - Method in class org.intermine.sql.writebatch.Batch
Flushes the batch out to the database server, then commits and re-opens the transaction, but does not guarantee that the operation is finished when this method returns.
batchCommitTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Request that the ObjectStoreWriter commits and closes the transaction and then opens a new one, without guaranteeing that the operation is finished before this method returns.
batchCommitTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Request that the ObjectStoreWriter commits and closes the transaction and then opens a new one, without guaranteeing that the operation is finished before this method returns.
batchCommitTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter
Request that the ObjectStoreWriter commits and closes the transaction and then opens a new one, without guaranteeing that the operation is finished before this method returns.
batchCommitTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Commits a transaction and opens a new one, without guaranteeing the operation is finished before this method returns.
batches - Variable in class org.intermine.objectstore.query.ResultsBatches
 
batchesCache - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
BatchingFetcher - Class in org.intermine.dataloader
Class providing EquivalentObjectFetcher functionality that batches fetches to improve performance.
BatchingFetcher(BaseEquivalentObjectFetcher, DataTracker, Source) - Constructor for class org.intermine.dataloader.BatchingFetcher
Constructor
batchQueried - Variable in class org.intermine.dataloader.BatchingFetcher
 
batchSize - Variable in class org.intermine.objectstore.query.ResultsBatches
 
BatchWriter - Interface in org.intermine.sql.writebatch
An interface representing an object that can flush a TableBatch to an SQL server Connection.
BatchWriterPostgresCopyImpl - Class in org.intermine.sql.writebatch
An implementation of the BatchWriter interface that uses PostgreSQL-specific COPY commands.
BatchWriterPostgresCopyImpl() - Constructor for class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
 
BatchWriterPreparedStatementImpl - Class in org.intermine.sql.writebatch
An implementation of the BatchWriter interface that uses JDBC PreparedStatement addBatch() and executeBatch() methods.
BatchWriterPreparedStatementImpl() - Constructor for class org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl
 
BatchWriterSimpleImpl - Class in org.intermine.sql.writebatch
An implementation of the BatchWriter interface that uses simple JDBC addBatch() and executeBatch() methods.
BatchWriterSimpleImpl() - Constructor for class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
BEDExporter - Class in org.intermine.bio.web.export
Exports LocatedSequenceFeature objects in UCSC BED format.
BEDExporter(PrintWriter, List<Integer>, String, String, boolean, String) - Constructor for class org.intermine.bio.web.export.BEDExporter
Constructor.
BEDExportForm - Class in org.intermine.bio.web.struts
Form for sequence export in BED format
BEDExportForm() - Constructor for class org.intermine.bio.web.struts.BEDExportForm
 
BEDHttpExporter - Class in org.intermine.bio.web.export
An implementation of TableHttpExporter that exports LocatedSequenceFeature objects in BED format.
BEDHttpExporter() - Constructor for class org.intermine.bio.web.export.BEDHttpExporter
 
BEDQueryService - Class in org.intermine.bio.webservice
A service for exporting query results in UCSC BED format.
BEDQueryService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.BEDQueryService
Constructor.
BEDQueryServlet - Class in org.intermine.bio.webservice
A servlet to hand off to the UCSC BED query service.
BEDQueryServlet() - Constructor for class org.intermine.bio.webservice.BEDQueryServlet
 
BEDRecord - Class in org.intermine.bio.io.bed
A record in a BED formatted file.
BEDRecord(String, int, int, String, int, String) - Constructor for class org.intermine.bio.io.bed.BEDRecord
Constructor The following five attributes are normally hosted in InterMine cases.
BEDUtil - Class in org.intermine.bio.web.export
Utility methods for UCSC BED format.
BeginAction - Class in org.intermine.web.struts
Prepare templates and news to be rendered on home page
BeginAction() - Constructor for class org.intermine.web.struts.BeginAction
 
beginTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Request that the ObjectStore begins a transaction, delegate to internal ObjectStoreWriter.
beginTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Request that the ObjectStoreWriter begins a transaction
beginTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter
Request that the ObjectStoreWriter begins a transaction
beginTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Begins a transaction.
beof - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
bestCandidate - Variable in class org.intermine.sql.precompute.BestQueryExplainer
 
BestQuery - Class in org.intermine.sql.precompute
This object is an abstract superclass for a Best Query tracker.
BestQuery() - Constructor for class org.intermine.sql.precompute.BestQuery
 
BestQueryException - Exception in org.intermine.sql.precompute
An Exception that may be thrown by an BestQuery.
BestQueryException() - Constructor for exception org.intermine.sql.precompute.BestQueryException
Constructs an BestQueryException
BestQueryException(String) - Constructor for exception org.intermine.sql.precompute.BestQueryException
Constructs an BestQueryException with the specified detail message.
BestQueryException(Throwable) - Constructor for exception org.intermine.sql.precompute.BestQueryException
Constructs an BestQueryException with the specified nested throwable.
BestQueryException(String, Throwable) - Constructor for exception org.intermine.sql.precompute.BestQueryException
Constructs an BestQueryException with the specified detail message and nested throwable.
BestQueryExplainer - Class in org.intermine.sql.precompute
Gets the database to explain each Query added and keeps hold of the best one so far.
BestQueryExplainer() - Constructor for class org.intermine.sql.precompute.BestQueryExplainer
Constructs an empty BestQueryExplainer for testing purposes
BestQueryExplainer(Connection, long) - Constructor for class org.intermine.sql.precompute.BestQueryExplainer
Constructs a BestQueryExplainer that will use the given Connection to explain Queries.
BestQueryExplainer.Candidate - Class in org.intermine.sql.precompute
A class representing a candidate optimised query.
BestQueryExplainer.Candidate(String) - Constructor for class org.intermine.sql.precompute.BestQueryExplainer.Candidate
Constructor.
BestQueryExplainer.Candidate(Query) - Constructor for class org.intermine.sql.precompute.BestQueryExplainer.Candidate
Constructor.
BestQueryExplainerVerbose - Class in org.intermine.sql.precompute
Gets the database to explain each Query added and keeps hold of the best one, logging all actions for the benefit of the IqlShell user.
BestQueryExplainerVerbose(Connection, long) - Constructor for class org.intermine.sql.precompute.BestQueryExplainerVerbose
Constructs an empty BestQueryExplainerVerbose.
BestQueryFallback - Class in org.intermine.sql.precompute
Gets the database to explain each Query added and keeps hold of the best one so far.
BestQueryFallback(Query, String) - Constructor for class org.intermine.sql.precompute.BestQueryFallback
Constructs a BestQueryFallback
BestQueryLogger - Class in org.intermine.sql.precompute
Logs each query added.
BestQueryLogger(boolean) - Constructor for class org.intermine.sql.precompute.BestQueryLogger
Constructs a BestQueryLogger
BestQueryStorer - Class in org.intermine.sql.precompute
Stores each query added.
BestQueryStorer() - Constructor for class org.intermine.sql.precompute.BestQueryStorer
Constructs a BestQueryStorer
bestQueryString - Variable in class org.intermine.sql.precompute.BestQueryLogger
 
betterThan(BestQueryExplainer.Candidate) - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
Returns true if the argument is slower than this, or if the argument is null.
BIG_BATCH_SIZE - Static variable in class org.intermine.api.results.WebResults
The batch size to use when we need to iterate through the whole result set.
BIG_BATCH_SIZE - Static variable in class org.intermine.bio.web.export.BEDHttpExporter
The batch size to use when we need to iterate through the whole result set.
BIG_BATCH_SIZE - Static variable in class org.intermine.bio.web.export.GFF3HttpExporter
The batch size to use when we need to iterate through the whole result set.
BIG_BATCH_SIZE - Static variable in class org.intermine.web.struts.SaveBagAction
The batch size to use when we need to iterate through the whole result set.
binderToFeatures - Variable in class org.intermine.webservice.server.complexes.ExportService.FeatureHolder
 
BioConverterUtil - Class in org.intermine.bio.util
Helper class for data converters.
BioDBConverter - Class in org.intermine.bio.dataconversion
A DBConverter with helper methods for bio sources.
BioDBConverter(Database, Model, ItemWriter, String, String) - Constructor for class org.intermine.bio.dataconversion.BioDBConverter
Create a new BioDBConverter object.
BioDBConverter(Database, Model, ItemWriter) - Constructor for class org.intermine.bio.dataconversion.BioDBConverter
Create a new BioDBConverter object.
BioDirectoryConverter - Class in org.intermine.bio.dataconversion
A DirectoryConverter that automatically sets the dataSets collection of objects as they are stored.
BioDirectoryConverter(ItemWriter, Model, String, String) - Constructor for class org.intermine.bio.dataconversion.BioDirectoryConverter
Create a new BioDirectoryConverter.
BioDirectoryConverter(ItemWriter, Model, String, String, String) - Constructor for class org.intermine.bio.dataconversion.BioDirectoryConverter
Create a new BioDirectoryConverter.
BioExportServlet - Class in org.intermine.bio.webservice
A servlet to hand off to the GFF3-query-service.
BioExportServlet() - Constructor for class org.intermine.bio.webservice.BioExportServlet
 
BioFileConverter - Class in org.intermine.bio.dataconversion
A FileConverter that automatically sets the dataSets collection of objects as they are stored.
BioFileConverter(ItemWriter, Model, String, String) - Constructor for class org.intermine.bio.dataconversion.BioFileConverter
Create a new BioFileConverter.
BioFileConverter(ItemWriter, Model, String, String, String) - Constructor for class org.intermine.bio.dataconversion.BioFileConverter
Create a new BioFileConverter.
BioFileConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.BioFileConverter
Create a new BioFileConverter.
BioGridConverter - Class in org.intermine.bio.dataconversion
DataConverter to parse biogrid data into items Genetic interactions are labeled protein interactions, so we can't store or create any objects until all experiments and interactors are processed.
BioGridConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.BioGridConverter
Constructor
BioGridConverter.Config - Class in org.intermine.bio.dataconversion
Represents configuration for a specific organism
BioGridConverter.Config() - Constructor for class org.intermine.bio.dataconversion.BioGridConverter.Config
 
BioGridConverter.ExperimentHolder - Class in org.intermine.bio.dataconversion
Holder object for Experiment.
BioGridConverter.ExperimentHolder() - Constructor for class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder
 
BioLinkRedirectManager - Class in org.intermine.bio.web
Contructs an alternate object details link pointing to an external URL for use in results table.
BioLinkRedirectManager(Properties) - Constructor for class org.intermine.bio.web.BioLinkRedirectManager
 
BioQueries - Class in org.intermine.bio.util
Bio utility methods for queries.
BioQueryService - Class in org.intermine.bio.webservice
A service for exporting query results as gff3.
BioQueryService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.BioQueryService
Constructor.
BioSequence - Class in org.intermine.bio.web.biojava
An implementation of the BioJava Sequence interface that uses InterMine objects underneath.
BioSequenceFactory - Class in org.intermine.bio.web.biojava
A factory for creating BioSequence objects.
BioSequenceFactory.SequenceType - Enum in org.intermine.bio.web.biojava
Type of sequences.
BioStoreHook - Class in org.intermine.bio.dataconversion
An implementation of DataConverterStoreHook that adds DataSet and DataSource references and collections to Items as they are stored.
BioStoreHook(Model, String, String, String) - Constructor for class org.intermine.bio.dataconversion.BioStoreHook
Create a new DataSetStoreHook object.
BioStoreHook(Model, String) - Constructor for class org.intermine.bio.dataconversion.BioStoreHook
Create a new DataSetStoreHook object.
BioUtil - Class in org.intermine.bio.util
Utility methods for the flymine package.
BioWidgetUtil - Class in org.intermine.bio.web.widget
Utility methods for the flymine package.
BioWidgetUtil() - Constructor for class org.intermine.bio.web.widget.BioWidgetUtil
Constructor (required for widgets)
BOOLEAN_KEYS - Static variable in class org.intermine.api.profile.UserPreferences
Common keys
BOOLEAN_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint
 
boring - Variable in class org.intermine.task.InheritanceDotTask
 
BOTH_FALSE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints as being both false.
BOTH_TRUE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints as being both true.
BrandingService - Class in org.intermine.webservice.server.branding
Serve branding information so that a client can provide a branded visual experience.
BrandingService(InterMineAPI) - Constructor for class org.intermine.webservice.server.branding.BrandingService
 
broken - Variable in class org.intermine.dataloader.DataTracker
 
bufferToHexString(byte[]) - Static method in class org.intermine.metadata.StringUtil
Convert a byte buffer to a hexadecimal string.
BuildBagAction - Class in org.intermine.web.struts
An action that makes a bag from text.
BuildBagAction() - Constructor for class org.intermine.web.struts.BuildBagAction
 
BuildBagForm - Class in org.intermine.web.struts
Form bean to represent the inputs needed to create a bag from user input.
BuildBagForm() - Constructor for class org.intermine.web.struts.BuildBagForm
 
BuildDbTask - Class in org.intermine.task
Generates and inserts SQL given database name, schema and temporary directory
BuildDbTask() - Constructor for class org.intermine.task.BuildDbTask
 
buildFile() - Method in class org.intermine.task.CreatePropertiesFile
build file
buildFromComponent(SqlGenerator.State, Query, DatabaseSchema, Map<Object, String>) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Builds the FROM list for the SQL query.
buildGroupBy(Query, DatabaseSchema, SqlGenerator.State) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Builds a String representing the GROUP BY component of the Sql query.
buildIndex(ObjectStore) - Method in class org.intermine.web.autocompletion.AutoCompleter
Build the index from the database blob
buildKeyStore() - Method in class org.intermine.web.security.KeyStoreBuilder
Build the key store.
buildObject(ResultSet, String, ObjectStoreInterMineImpl, Class<?>, Set<String>) - Static method in class org.intermine.objectstore.intermine.ResultsConverter
Builds an object from separate fields in flat mode.
buildOrderBy(SqlGenerator.State, Query, DatabaseSchema, int) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Builds a String representing the ORDER BY component of the Sql query.
buildQueryValue(PathConstraint) - Method in class org.intermine.web.logic.widget.WidgetLdr
Return a QueryValue instance using the path contraint given in input
buildSelectComponent(SqlGenerator.State, Query, DatabaseSchema, int) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Builds a String representing the SELECT component of the Sql query.
buildTree(String) - Method in class org.intermine.web.logic.querybuilder.ModelBrowserHelper.NodeBuilder
Recurse through the model and build a tree of metadata nodes based on this
buildWhereClause(SqlGenerator.State, Query, Constraint, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Builds the WHERE clause for the SQL query.

C

cache - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
CACHE_LARGEST_OBJECT - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
CacheHoldingArrayList<E> - Class in org.intermine.util
This is an extension of the the ArrayList class, designed to be used by systems that return Lists of data, with extra data that should not be flushed out of a cache until the List is garbage collected.
CacheHoldingArrayList() - Constructor for class org.intermine.util.CacheHoldingArrayList
Empty constructor
CacheHoldingArrayList(Collection<E>) - Constructor for class org.intermine.util.CacheHoldingArrayList
Constructs a new instance from another Collection.
CacheHoldingArrayList(int) - Constructor for class org.intermine.util.CacheHoldingArrayList
Constructs a new instance with the given initial capacity.
cacheLines - Variable in class org.intermine.sql.precompute.OptimiserCache
A Map that holds a mapping from unoptimised query string (with LIMIT and OFFSET stripped off) to a Set of OptimiserCacheLine objects.
cacheLinks(MultiKey, Collection<PartnerLink>) - Method in class org.intermine.api.mines.FriendlyMineManager
 
CacheMap<K,V> - Class in org.intermine.util
This is a Map implementation designed specifically for people intending to create a cache.
CacheMap(int, float) - Constructor for class org.intermine.util.CacheMap
Constructs a new, empty CacheMap with the given initial capacity and the given load factor.
CacheMap(int) - Constructor for class org.intermine.util.CacheMap
Constructs a new, empty CacheMap with the given initial capacity and the default load factor, which is 0.75.
CacheMap() - Constructor for class org.intermine.util.CacheMap
Constructs a new, empty CacheMap with the default initial capacity (16) and the default load factor (0.75).
CacheMap(String) - Constructor for class org.intermine.util.CacheMap
Constructs a new, empty CacheMap with the default initial capacity (16) and the default load factor (0.75), and a name.
CacheMap(Map<K, V>) - Constructor for class org.intermine.util.CacheMap
Constructs a new CacheMap with the same mappings as the specified Map.
cacheMisses - Variable in class org.intermine.dataloader.BatchingFetcher
 
cacheObjectById(Integer, InterMineObject) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Places an entry into the objectstore getObjectById cache.
cacheObjectById(Integer, InterMineObject) - Method in interface org.intermine.objectstore.ObjectStore
Places an entry into the objectstore getObjectById cache.
cacheObjectById(Integer, InterMineObject) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Places an entry into the objectstore getObjectById cache.
cacheObjectById(Integer, InterMineObject) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Places an entry into the objectstore getObjectById cache.
calcThisProjectName() - Method in class org.intermine.task.Dependencies
Return the project name calculated from the path of this project.
calculate(EnrichmentInput, Double, String, boolean, CorrectionCoefficient) - Static method in class org.intermine.web.logic.widget.EnrichmentCalculation
Perform an enrichment calculation based on input from some source and return results that include a p-value and count for each attribute that was observed in the sample.
CalculateLocations - Class in org.intermine.bio.postprocess
Calculate additional mappings between annotation after loading into genomic ObjectStore.
CalculateLocations(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.CalculateLocations
Create a new CalculateLocations object from an ObjectStoreWriter
CalculateLocations.SimpleLoc - Class in org.intermine.bio.postprocess
Lightweight representation of a Location for easier manipulation and storing in maps.
CalculateLocations.SimpleLoc(int, int, int, int, String) - Constructor for class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
Construct with integer values
CalculateLocations.SimpleLoc(int, int, Location) - Constructor for class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
Construct with integer values for object and subject and a Location object
call(Either<A, B>) - Method in class org.intermine.webservice.server.core.EitherVisitor
 
call(A) - Method in class org.intermine.webservice.server.core.F
The body of the function
call(X) - Method in class org.intermine.webservice.server.core.F.Constant
Call this function, returning the value supplied to the constructor.
call(A) - Method in interface org.intermine.webservice.server.core.Function
Take an A and return a B.
call(T) - Method in interface org.intermine.webservice.server.core.Predicate
Apply some test to some kind of thing.
call(String) - Method in class org.intermine.webservice.server.core.RateLimitHistory
 
Callback - Class in org.intermine.web.struts.oauth2
The controller that handles the requests made after the user has visited their authorisation provider to log-in.
Callback() - Constructor for class org.intermine.web.struts.oauth2.Callback
 
CALLBACK_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
The callback to be supplied for jsonp calls
canAssignObjectToType(Class<?>, InterMineObject) - Static method in class org.intermine.api.util.PathUtil
Return true if given type (of a constraint) can be assigned to the InterMineObject - i.e.
cancelRequest(Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
This method cancels any Statement running in a given request ID, and blacklists that ID.
candidates - Variable in class org.intermine.sql.precompute.BestQueryExplainer
 
candidateTables - Variable in class org.intermine.sql.precompute.BestQueryExplainer
 
canDoPkNow(PrimaryKey, ClassDescriptor, Map<PrimaryKey, ClassDescriptor>) - Method in class org.intermine.dataloader.BatchingFetcher
Returns whether this primary key can be fetched now.
canExport(List<Class<?>>) - Method in class org.intermine.bio.web.export.BEDExporter
 
canExport(PagedTable) - Method in class org.intermine.bio.web.export.BEDHttpExporter
Check if this TableExporter can export the given PagedTable.
canExport(List<Class<?>>) - Method in class org.intermine.bio.web.export.GAFExporter
 
canExport(List<Class<?>>) - Method in class org.intermine.bio.web.export.GFF3Exporter
This method finds out if result row composed from instances of these classes can be exported with actual implementation of exporter.
canExport(PagedTable) - Method in class org.intermine.bio.web.export.GFF3HttpExporter
Check if this TableExporter can export the given PagedTable.
canExport(List<Class<?>>) - Method in class org.intermine.bio.web.export.SequenceExporter
This method finds out if result row composed from instances of these classes can be exported with actual implementation of exporter.
canExport(PagedTable) - Method in class org.intermine.bio.web.export.SequenceHttpExporter
Check if this TableExporter can export the given PagedTable.
canExport(PagedTable) - Method in class org.intermine.model.testmodel.web.EmployeeExporter
Check if this TableExporter can export the given PagedTable.
canExport(List<Class<?>>) - Method in interface org.intermine.web.logic.export.Exporter
This method finds out if result row composed from instances of these classes can be exported with actual implementation of exporter.
canExport(List<Class<?>>) - Method in class org.intermine.web.logic.export.ExporterImpl
This method finds out if result row composed from instances of these classes can be exported with actual implementation of exporter.
canExport(PagedTable, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper
Return true if the specified class or a subclass is found in a column of the paged table (or is the parent class of a field displayed in the table).
canExport(PagedTable) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter
 
canExport(PagedTable) - Method in interface org.intermine.web.logic.export.http.TableHttpExporter
Check if this TableExporter can export the given PagedTable.
canExportStatic(List<Class<?>>) - Static method in class org.intermine.bio.web.export.BEDExporter
 
canExportStatic(List<Class<?>>) - Static method in class org.intermine.bio.web.export.GAFExporter
 
canExportStatic(List<Class<?>>) - Static method in class org.intermine.bio.web.export.GFF3Exporter
 
canExportStatic(List<Class<?>>) - Static method in class org.intermine.bio.web.export.SequenceExporter
 
canHaveCollection(String) - Method in class org.intermine.xml.full.Item
Return true if and only if the argument names a possible collection for this Item.
canHaveReference(String) - Method in class org.intermine.xml.full.Item
Return true if and only if the argument names a possible reference for this Item.
canonicaliseIndexes(Collection<String>) - Static method in class org.intermine.sql.precompute.PrecomputedTableManager
Takes a collection of index strings, and removes redundant entries.
canServe(Format) - Method in class org.intermine.webservice.server.lists.AvailableListsService
 
canServe(Format) - Method in class org.intermine.webservice.server.lists.ListMakerService
 
canServe(Format) - Method in class org.intermine.webservice.server.model.ModelService
 
canServe(Format) - Method in class org.intermine.webservice.server.path.PossibleValuesService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.CodeService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.QueryRemovalService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.QueryRetrieverService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.QueryToListService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.QueryUploadService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.result.QueryResultService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.result.TableRowService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.SavedQueryRetrievalService
 
canServe(Format) - Method in class org.intermine.webservice.server.template.AvailableTemplatesService
 
canServe(Format) - Method in class org.intermine.webservice.server.template.SingleTemplateService
 
canServe(Format) - Method in class org.intermine.webservice.server.template.TemplateRemovalService
 
canServe(Format) - Method in class org.intermine.webservice.server.template.TemplateUploadService
 
canServe(Format) - Method in class org.intermine.webservice.server.VersionService
 
canServe(Format) - Method in class org.intermine.webservice.server.WebService
Check whether the format is acceptable.
canServe(Format) - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService
 
capitalise(String) - Static method in class org.intermine.metadata.StringUtil
Returns a capitalised version of the given String
castBagsToCommonType(Collection<InterMineBag>, String, Set<String>, Profile, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils
Given a common type, return a collection of bags cast to that type.
CATEGORIES - Static variable in class org.intermine.web.logic.Constants
ServletContext attribute, List of category names.
categoriseBasedOnTags(FieldDescriptor, String, DisplayField, Map<String, DisplayField>, TagManager, String, Map<String, Map<String, DisplayField>>, boolean) - Static method in class org.intermine.web.struts.ReportController
For a given FieldDescriptor, look up its 'aspect:' tags and place it in the correct map within placementRefsAndCollections.
categorizeFeatureTypes(Set<String>, GenomicRegion) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Get all feature types from a list of sequence features
category - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
caughtError - Variable in class org.intermine.bio.dataconversion.IdResolverFactory
 
CEIL - Static variable in class org.intermine.objectstore.query.QueryFunction
Smallest integer value greater than input.
ChadoCV - Class in org.intermine.bio.chado
Objects of this class represent a controlled vocabulary from chado.
ChadoCV(String) - Constructor for class org.intermine.bio.chado.ChadoCV
Create a new ChadoCV.
ChadoCVFactory - Class in org.intermine.bio.chado
A factory for ChadoCV objects.
ChadoCVFactory(Connection) - Constructor for class org.intermine.bio.chado.ChadoCVFactory
Create a new ChadoCVFactory.
ChadoCVTerm - Class in org.intermine.bio.chado
Objects of this class represent one row of the chado cvterm table.
ChadoCVTerm(String) - Constructor for class org.intermine.bio.chado.ChadoCVTerm
Create a new cv term object
ChadoDBConverter - Class in org.intermine.bio.dataconversion
DataConverter to read from a Chado database into items
ChadoDBConverter(Database, Model, ItemWriter) - Constructor for class org.intermine.bio.dataconversion.ChadoDBConverter
Create a new ChadoDBConverter object.
ChadoProcessor - Class in org.intermine.bio.dataconversion
A processor for a chado module.
ChadoProcessor(ChadoDBConverter) - Constructor for class org.intermine.bio.dataconversion.ChadoProcessor
Create a new ChadoModuleProcessor object.
ChangeEvent - Interface in org.intermine.api.search
Events that represent changes in something.
ChangePasswordAction - Class in org.intermine.web.struts
 
ChangePasswordAction() - Constructor for class org.intermine.web.struts.ChangePasswordAction
 
ChangePasswordForm - Class in org.intermine.web.struts
Form bean to represent the inputs needed to change a password from user input.
ChangePasswordForm() - Constructor for class org.intermine.web.struts.ChangePasswordForm
 
changePasswordWithToken(String, String) - Method in class org.intermine.api.profile.ProfileManager
Changes the password of a profile if the given token is valid.
changePath(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Change the currently active metadata Node
changeSequence(Set<Object>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Increments the sequence numbers for the given set of database components.
ChangeTableAction - Class in org.intermine.web.struts
Implementation of DispatchAction.
ChangeTableAction() - Constructor for class org.intermine.web.struts.ChangeTableAction
 
ChangeTableSizeAction - Class in org.intermine.web.struts
Changes the size of the results displayed.
ChangeTableSizeAction() - Constructor for class org.intermine.web.struts.ChangeTableSizeAction
 
ChangeTableSizeForm - Class in org.intermine.web.struts
Form bean for changing the page size.
ChangeTableSizeForm() - Constructor for class org.intermine.web.struts.ChangeTableSizeForm
Constructor
changeViewPathDescription(String, String) - Method in class org.intermine.dwr.AjaxServices
Set the description of a view path.
characters(char[], int, int) - Method in class org.intermine.api.bag.BagQueryHandler
characters(char[], int, int) - Method in class org.intermine.api.bag.InvitationHandler
characters(char[], int, int) - Method in class org.intermine.api.profile.PreferencesHandler
characters(char[], int, int) - Method in class org.intermine.pathquery.PathQueryHandler
characters(char[], int, int) - Method in class org.intermine.webservice.server.ServiceListingHandler
 
charAt(int) - Method in class org.intermine.bio.util.ClobAccessReverseComplement
Return a character from the specified index.
charAt(int) - Method in class org.intermine.model.StringConstructor
charAt(int) - Method in class org.intermine.objectstore.query.ClobAccess
Return a character from the specified index.
charAt(int) - Method in class org.intermine.objectstore.query.PendingClob
Return a character from the specified index.
ChartRenderer - Class in org.flymine.web
Graph the microarray results for a particular gene/experiment
ChartRenderer() - Constructor for class org.flymine.web.ChartRenderer
 
check(Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.precompute.OptimiserMappingChecker
Checks a partial mapping.
check(Map<T, T>) - Method in interface org.intermine.util.MappingUtilChecker
Checks a partial mapping.
checkAttribute(String) - Method in class org.intermine.xml.full.Item
Return true if the name parameter is an attribute of the class for this Item or if the Model or the className of this Item haven't been set.
checkCollection(String) - Method in class org.intermine.xml.full.Item
Throw a RuntimeException if the name parameter isn't an collection in the class set by setClassName() in the Model set by setModel().
checkComparisonEquals(int) - Static method in class org.intermine.sql.query.AbstractConstraint
Take an integer as if it was created by compare, and return true if this implies that the left constraint is EQUAL to the right constraint, in a loose sense.
checkComparisonImplies(int) - Static method in class org.intermine.sql.query.AbstractConstraint
Take an integer as if it was created by compare, and return true if this implies that the left constraint IMPLIES the right constraint, in a loose sense.
checkFieldExists(Model, String, String, String) - Static method in class org.intermine.bio.postprocess.PostProcessUtil
Check that a class exists and has a field of the given name.
CheckForIsNotNullConstraint - Class in org.intermine.objectstore.intermine
For use with ConstraintHelper.traverseConstraints().
CheckForIsNotNullConstraint(QueryNode) - Constructor for class org.intermine.objectstore.intermine.CheckForIsNotNullConstraint
Construct with the QueryNode to test for NOT NULL constraint.
checkImplementations(String) - Method in class org.intermine.xml.full.Item
Throw RuntimeException if the given implementations don't match the model.
checkLists(Map<String, InterMineBag>, List<String>) - Method in class org.intermine.webservice.server.lists.ListInput
Make sure that any lists names exist.
checkPassword(String, String) - Static method in class org.intermine.util.PasswordHasher
Checks to see if a password matches an optionally hashed password entry.
checkPathFormat(String) - Static method in class org.intermine.pathquery.PathQuery
Verifies the format of a path for a query.
checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.AbstractRegionExportService
No-op stub.
checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.BEDQueryService
 
checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.BioQueryService
No-op stub.
checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.FastaQueryService
 
checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.GAFQueryService
 
checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.GenomicRegionBedService
 
checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.GenomicRegionFastaService
 
checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.GenomicRegionGFF3Service
 
checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.GFFQueryService
 
checkReference(String) - Method in class org.intermine.xml.full.Item
Throw a RuntimeException if the name parameter isn't an reference in the class set by setClassName() in the Model set by setModel().
checkResponse() - Method in class org.intermine.webservice.client.util.HttpConnection
Called to check the response and generate an appropriate exception (on failure).
checkSequence(Map<Object, Integer>, Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Checks a number against the sequence number, and throws an exception if they do not match.
checkSequence(Map<Object, Integer>, Query, String) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Checks a number against the sequence number, and throws an exception if they do not match.
checkStartLimit(int, int, Query) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Checks the start and limit to see whether they are inside the hard limits for this ObjectStore
checkTaxonId(String, String) - Method in class org.intermine.bio.dataconversion.IdResolver
Check that the given taxon id has some data for it. if an exception thrown, there must be something wrong with resolver factory.
ChromosomeInfo - Class in org.intermine.bio.web.model
This Java bean stores the information for span validation use.
ChromosomeInfo() - Constructor for class org.intermine.bio.web.model.ChromosomeInfo
 
ChromosomeLocationHelper - Class in org.intermine.bio.query.range
Method to help querying for ranges
ChromosomeLocationHelper() - Constructor for class org.intermine.bio.query.range.ChromosomeLocationHelper
Method to set up chromosome fields for helping
CLASS - Static variable in class org.intermine.api.tag.TagTypes
A Class/ClassDescriptor.
CLASS_KEYS - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key to use to store the class_keys.properties file.
ClassChooserController - Class in org.intermine.web.struts
Gets list of help text blurbs for each class, and passes them on to the display page.
ClassChooserController() - Constructor for class org.intermine.web.struts.ClassChooserController
 
ClassConstraint - Class in org.intermine.objectstore.query
Constrain whether a QueryClass is equal/not equal to another QueryClass or an example of an object belonging to a QueryClass.
ClassConstraint(QueryClass, ConstraintOp, QueryClass) - Constructor for class org.intermine.objectstore.query.ClassConstraint
Construct ClassConstraint
ClassConstraint(QueryClass, ConstraintOp, InterMineObject) - Constructor for class org.intermine.objectstore.query.ClassConstraint
Construct ClassConstraint
classConstraintToString(SqlGenerator.State, StringBuffer, ClassConstraint, Query, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a ClassConstraint object into a String suitable for putting in an SQL query.
ClassDescriptor - Class in org.intermine.metadata
Describe a business model class.
ClassDescriptor(String, String, boolean, Collection<AttributeDescriptor>, Collection<ReferenceDescriptor>, Collection<CollectionDescriptor>) - Constructor for class org.intermine.metadata.ClassDescriptor
Construct a ClassDescriptor.
ClassKeyHelper - Class in org.intermine.api.config
Methods to read and manage keys for classes.
classKeys - Variable in class org.intermine.api.InterMineAPI
 
ClassKeys - Interface in org.intermine.api.types
Type alias for classkeys - simplifies matters and prevents mistakes.
ClassKeyServlet - Class in org.intermine.webservice.server
A Servlet for routing requests to the ClassKeyService.
ClassKeyServlet() - Constructor for class org.intermine.webservice.server.ClassKeyServlet
 
ClassKeysNotFoundException - Exception in org.intermine.api.bag
Exception thrown when given attempting to create a bag for a type that isn't in the model, this can happen when reading bags from a userprofile database and the data model has changed.
ClassKeysNotFoundException(String) - Constructor for exception org.intermine.api.bag.ClassKeysNotFoundException
Constructs an IncompatibleBagTypesException with the specified detail message.
ClassKeysNotFoundException(Throwable) - Constructor for exception org.intermine.api.bag.ClassKeysNotFoundException
Constructs an IncompatibleBagTypesException with the specified nested throwable.
ClassKeysNotFoundException(String, Throwable) - Constructor for exception org.intermine.api.bag.ClassKeysNotFoundException
Constructs an IncompatibleBagTypesException with the specified detail message and nested throwable.
ClassKeysService - Class in org.intermine.webservice.server
A service to fetch a JSON representation of class keys for all classes in the model.
ClassKeysService(InterMineAPI) - Constructor for class org.intermine.webservice.server.ClassKeysService
Construct with the InterMineAPI.
className - Variable in class org.intermine.objectstore.intermine.TorqueModelOutput
 
className - Variable in class org.intermine.web.struts.QueryClassSelectForm
 
classNotExists(Class<? extends FastPathObject>) - Method in class org.intermine.dataloader.EquivalentObjectHints
Returns true if there were no instances of the given class in the database.
ClassResourceOpener - Class in org.intermine.web.logic
Objects that open resources relative to a classpath.
ClassResourceOpener(Class<?>) - Constructor for class org.intermine.web.logic.ClassResourceOpener
Constructor.
classToType(Class<?>) - Static method in class org.intermine.objectstore.query.UnknownTypeValue
Converts a Class into an approximate type.
cld - Variable in class org.intermine.metadata.FieldDescriptor
 
clean() - Method in class org.intermine.dataloader.ObjectDescription
Marks the ObjectDescription as clean - that is all the data has been flushed to the backing database.
cleanTags(TagManager) - Static method in class org.intermine.web.struts.InitialiserPlugin
Remove class tags from the user profile that refer to classes that non longer exist
cleanUp() - Method in class org.intermine.webservice.server.WebService
Subclasses may put clean-up code here, to be run after the request has been executed.
clear() - Method in class org.intermine.api.profile.UserPreferences
 
clear() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Remove all items held locally in handler.
clear() - Method in class org.intermine.dataloader.DataTracker
Clears the data tracker of all entries.
clear() - Method in class org.intermine.sql.writebatch.Batch
Clears the batch without writing it to the database.
clear() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Clears the batch.
clear() - Method in interface org.intermine.sql.writebatch.Table
Clears the batch.
clear() - Method in class org.intermine.sql.writebatch.TableBatch
Clears the batch.
clear() - Method in class org.intermine.util.AlwaysMap
clear() - Method in class org.intermine.util.IdentityMap
clear() - Method in class org.intermine.util.IntPresentSet
Removes all ints from the object.
clear() - Method in class org.intermine.util.IntToIntMap
Removes all mappings from the object.
clear() - Method in class org.intermine.util.PseudoSet
clear() - Method in class org.intermine.util.ReferenceMap
clear() - Method in class org.intermine.webservice.client.results.ResultRowList
 
clearCache() - Method in class org.intermine.webservice.client.core.Service
Clear the cache on this object.
clearCache() - Method in class org.intermine.webservice.client.services.ModelService
 
clearConstraints() - Method in class org.intermine.pathquery.PathQuery
Clears the entire set of constraints from this query, and resets the constraint logic.
clearConstraints() - Method in class org.intermine.template.TemplateQuery
Clears the entire set of constraints from this query, and resets the constraint logic.
clearDataSetReferenceList() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Reset the list of DataSet items.
clearDescriptions() - Method in class org.intermine.pathquery.PathQuery
Removes all path descriptions from this query.
clearFinalItems() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Clear the list of final items.
clearLocation() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Clear the location item for this record.
clearObj(Integer) - Method in class org.intermine.dataloader.DataTracker
Clears the cache for a particular object, in preparation for writing all the data for that object.
clearOrderBy() - Method in class org.intermine.objectstore.query.Query
Clears the ORDER BY clause of this Query
clearOrderBy() - Method in class org.intermine.pathquery.PathQuery
Clears the entire order by list.
clearOuterJoinStatus() - Method in class org.intermine.pathquery.PathQuery
Clears all outer join status data from this query.
clearProblem() - Method in class org.intermine.sql.writebatch.Batch
Clears the problem with the Batch.
clearPublicationReferenceList() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Reset the list of Publication items.
clearSelect() - Method in class org.intermine.objectstore.query.Query
Clears the SELECT list
clearSelectIds() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Clear the table selection
clearView() - Method in class org.intermine.pathquery.PathQuery
Clears the entire view list.
Clob - Class in org.intermine.objectstore.query
Object representing a large String that has been stored in the database.
Clob(int) - Constructor for class org.intermine.objectstore.query.Clob
Constructs a new Clob.
clob - Variable in class org.intermine.objectstore.query.ClobAccess
 
CLOB_PAGE_SIZE - Static variable in class org.intermine.objectstore.query.Clob
Page size for clob data
CLOB_TABLE_NAME - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the table that stores Clobs.
ClobAccess - Class in org.intermine.objectstore.query
Class used to read a Clob from the ObjectStore.
ClobAccess() - Constructor for class org.intermine.objectstore.query.ClobAccess
Protected constructor for use by PendingClob only.
ClobAccess(ObjectStore, Clob) - Constructor for class org.intermine.objectstore.query.ClobAccess
Construct a ClobAccess object from an ObjectStore and a Clob.
ClobAccess.ClobAccessSubclassFactory - Class in org.intermine.objectstore.query
Class to provide fast access to the constructor of plugin subclasses of ClobAccess.
ClobAccess.ClobAccessSubclassFactory() - Constructor for class org.intermine.objectstore.query.ClobAccess.ClobAccessSubclassFactory
 
ClobAccessReverseComplement - Class in org.intermine.bio.util
Subclass of ClobAccess that reverses and complements the DNA sequence contained within it.
ClobAccessReverseComplement(ClobAccess) - Constructor for class org.intermine.bio.util.ClobAccessReverseComplement
Construct this object from an existing ClobAccess object
CLOBID_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the clobid column in the clob table.
CLOBPAGE_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the page number column in the clob table.
CLOBVAL_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the value column in the clob table.
clone() - Method in class org.intermine.api.profile.InterMineBag
Create copy of bag.
clone() - Method in class org.intermine.api.template.ApiTemplate
Clone this ApiQuery
clone() - Method in class org.intermine.pathquery.PathQuery
Returns a deep copy of this object.
clone() - Method in class org.intermine.template.TemplateQuery
Clone this TemplateQuery.
cloneAttributeDescriptors(Set<AttributeDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger
Clone a set of AttributeDescriptors.
cloneClassDescriptor(ClassDescriptor) - Static method in class org.intermine.modelproduction.ModelMerger
Construct a ClassDescriptor that takes on all the properties of cld without attaching to a particular Model.
cloneCollectionDescriptors(Set<CollectionDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger
Clone a set of CollectionDescriptors.
cloneInterMineObject(O) - Static method in class org.intermine.bio.postprocess.PostProcessUtil
Create a clone of given InterMineObject including the id.
cloneQuery(Query) - Static method in class org.intermine.objectstore.query.QueryCloner
Clones a query object.
cloneReferenceDescriptors(Set<ReferenceDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger
Clone a set of ReferenceDescriptors.
cloneWithoutEditableConstraints() - Method in class org.intermine.template.TemplateQuery
Return a clone of this template query with all editable constraints removed - i.e. a query that will return all possible results of executing the template.
close() - Method in class org.intermine.api.bag.BagManager
Close the TagManager
close() - Static method in class org.intermine.api.lucene.KeywordSearch
set all the variables to NULL
close() - Method in class org.intermine.api.profile.ProfileManager
Close this ProfileManager
close() - Method in class org.intermine.api.profile.TagManager
Close this TagManager.
close() - Method in class org.intermine.api.tracker.TrackerDelegate
Release the db connection when done.
close() - Method in class org.intermine.bio.dataconversion.BioGridConverter
Perform any necessary clean-up after processing
close() - Method in class org.intermine.bio.dataconversion.GFF3Converter
Perform any necessary clean-up after post-conversion
close() - Method in class org.intermine.bio.dataconversion.KeggPathwayConverter
Perform any necessary clean-up after processing
close() - Method in class org.intermine.bio.dataconversion.ReactomeConverter
Perform any necessary clean-up after processing
close() - Method in class org.intermine.dataconversion.DataConverter
Perform any necessary clean-up after processing
close() - Method in class org.intermine.dataconversion.DirectoryConverter
Perform any necessary clean-up after post-conversion
close() - Method in interface org.intermine.dataconversion.ItemWriter
Flushes any store queue, closes transactions, and generally makes sure that every Item passed to the store() method is committed to the destination.
close() - Method in class org.intermine.dataconversion.MockItemWriter
Flushes any store queue, closes transactions, and generally makes sure that every Item passed to the store() method is committed to the destination.
close() - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
Flushes any store queue, closes transactions, and generally makes sure that every Item passed to the store() method is committed to the destination.
close(Source) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Close method - prints out summary data.
close(Source) - Method in class org.intermine.dataloader.BatchingFetcher
Close method - prints out summary data.
close() - Method in class org.intermine.dataloader.DataTracker
Closes this DataTracker, releasing both connections to the database.
close() - Method in class org.intermine.dataloader.DirectDataLoader
Close the DirectDataLoader, must be called to make sure final batch of data is stored.
close(Source) - Method in class org.intermine.dataloader.HintingFetcher
Close method - prints out summary data.
close() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Closes the connection associated with this ObjectStoreWriter
close() - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Closes the connection associated with this ObjectStoreWriter
close(Source) - Method in class org.intermine.dataloader.ParallelBatchingFetcher
Close method - prints out summary data.
close() - Method in class org.intermine.dataloader.XmlDataLoader
Perform any necessary clean-up and close the integration writer
close() - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream
 
close() - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream
 
close() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Closes this ObjectStore's DB log connection.
close() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Closes this ObjectStore's DB log connection.
close() - Method in interface org.intermine.objectstore.ObjectStoreWriter
Closes the connection associated with this ObjectStoreWriter
close() - Method in class org.intermine.sql.logging.DatabaseWriter
Close this Writer
close(Connection) - Method in class org.intermine.sql.writebatch.Batch
Closes this BatchWriter.
close() - Method in class org.intermine.webservice.client.util.HttpConnection
Closes connection.
closeIndexWriter() - Method in class org.intermine.web.autocompletion.LuceneIndex
close the current indexWriter
closeSituation - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
cls - Variable in class org.intermine.objectstore.query.ContainsConstraint
 
cls - Variable in class org.intermine.objectstore.query.SubqueryConstraint
 
clsCol - Variable in class org.intermine.bio.dataconversion.IdResolverFactory
 
clsName - Variable in class org.intermine.task.AnalyseDbTask
 
clsName - Variable in class org.intermine.task.DirectoryConverterTask
 
clsName - Variable in class org.intermine.task.FileConverterTask
 
clsName - Variable in class org.intermine.task.PostProcessorTask
 
COALESCE - Static variable in class org.intermine.sql.query.Function
COALESCE operator - used by the precomputed tables' orderby fields.
CodeService - Class in org.intermine.webservice.server.query
A service for generating code based on a query.
CodeService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.CodeService
Constructor.
CodeServlet - Class in org.intermine.webservice.server.query
A servlet for routing requests to the code service.
CodeServlet() - Constructor for class org.intermine.webservice.server.query.CodeServlet
 
CodeTranslator - Class in org.intermine.webservice.server
Translates strings between codes used in ConstraintOp class and abbreviations or full code names of operations.
collapse(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TreeAction
Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
COLLECTION - Static variable in class org.intermine.api.tag.TagTypes
Collection.
CollectionDescriptor - Class in org.intermine.metadata
Describes a field that references a collection of other objects.
CollectionDescriptor(String, String, String) - Constructor for class org.intermine.metadata.CollectionDescriptor
Construct a CollectionDescriptor.
CollectionDetailsAction - Class in org.intermine.web.struts
Action that creates a table of collection elements for display.
CollectionDetailsAction() - Constructor for class org.intermine.web.struts.CollectionDetailsAction
 
CollectionTableAction - Class in org.intermine.web.struts
Action that creates a table of collection elements for display in a table widget.
CollectionTableAction() - Constructor for class org.intermine.web.struts.CollectionTableAction
 
collectionToSQLString(Collection<? extends SQLStringable>, String) - Static method in class org.intermine.sql.query.Query
Converts a collection of objects that implement the getSQLString method into a String, with the given comma string between each element.
collectionToSQLString(Collection<? extends SQLStringable>, Collection<String>, String) - Static method in class org.intermine.sql.query.Query
Converts a collection of objects that implement the getSQLString method into a String, with the given comma string between each element.
CollectionUtil - Class in org.intermine.util
Utilities for Collections.
colonsToDots(String) - Static method in class org.intermine.metadata.StringUtil
Converts all the colons in a String into dots.
Column - Class in org.intermine.api.results
Configuration information for a column in a table
Column(Path, String, int, Class) - Constructor for class org.intermine.api.results.Column
Constructor that takes a Path object.
Column(Path, int, Class) - Constructor for class org.intermine.api.results.Column
Constructor that takes a Path object.
Column(String, int, Class) - Constructor for class org.intermine.api.results.Column
Constructor that takes a String name.
COLUMN_HEADERS - Static variable in class org.intermine.webservice.server.output.FlatFileFormatter
The key for the header columns
columnExists(Connection, String, String) - Static method in class org.intermine.sql.DatabaseUtil
Tests if a column exists in the database
columnFullNames - Variable in class org.intermine.web.logic.results.InlineResultsTable
 
ColumnHeaderStyle - Enum in org.intermine.webservice.server
Enumeration for outer join status.
columnId - Variable in class org.intermine.api.results.Column
 
combineBags() - Method in class org.intermine.api.bag.operations.BagOperation
 
combineBags() - Method in class org.intermine.api.bag.operations.RelativeComplement
 
CombinedIterator<E> - Class in org.intermine.util
An Iterator that combines the contents of various other Iterators.
CombinedIterator(List<Iterator<? extends E>>) - Constructor for class org.intermine.util.CombinedIterator
Constructs a CombinedIterator from a List of Iterators.
combineWith(ProfileMergeIssues) - Method in class org.intermine.web.logic.profile.ProfileMergeIssues
Combine this set of merge issues with another set.
CommaFieldExporter - Class in org.intermine.model.testmodel.web
CommaFieldExporter class
CommaFieldExporter() - Constructor for class org.intermine.model.testmodel.web.CommaFieldExporter
 
Command - Class in org.intermine.webservice.server.jbrowse
 
Command(Commands.Action, String, String, Segment, Map<String, String>) - Constructor for class org.intermine.webservice.server.jbrowse.Command
 
CommandRunner - Class in org.intermine.webservice.server.jbrowse
 
CommandRunner(InterMineAPI) - Constructor for class org.intermine.webservice.server.jbrowse.CommandRunner
 
Commands - Class in org.intermine.webservice.server.jbrowse
 
Commands.Action - Enum in org.intermine.webservice.server.jbrowse
 
comment - Variable in class org.intermine.template.TemplateQuery
The private comment for this query.
commitTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Request that the ObjectStore commits and closes the transaction, delegate to internal ObjectStoreWriter.
commitTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Request that the ObjectStoreWriter commits and closes the transaction
commitTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter
Request that the ObjectStoreWriter commits and closes the transaction
commitTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Commits a transaction.
COMMON_KEYS - Static variable in class org.intermine.api.profile.UserPreferences
Common keys
CommutativeOperationInput - Class in org.intermine.webservice.server.lists
An input class for operations that are commutative.
CommutativeOperationInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.CommutativeOperationInput
Constructor.
CompanyDistLdr - Class in org.intermine.model.testmodel.web.widget
 
CompanyDistLdr(InterMineBag, ObjectStore, String) - Constructor for class org.intermine.model.testmodel.web.widget.CompanyDistLdr
 
comparable(Class<?>, Class<?>) - Static method in class org.intermine.objectstore.query.SimpleConstraint
Check whether the two arguments are of comparable types i.e. they are of similiar type and we know how to handle that type
compare(String, String) - Method in class org.intermine.api.bag.BagManager.ByTagOrder
 
compare(String, String) - Method in class org.intermine.api.bag.BagManager.CaseInsensitiveComparator
 
compare(String, String) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ByPValueComparator
 
compare(String, String) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ByTStatisticComparator
 
compare(String, String) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.CaseInsensitiveComparator
 
compare(String, String) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ByPValueComparator
 
compare(String, String) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ByTStatisticComparator
 
compare(String, String) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.CaseInsensitiveComparator
 
compare(String, String) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ByCellCountComparator
 
compare(String, String) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ByLevelComparator
 
compare(String, String) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ByOverallLevelComparator
 
compare(InterMineObject, InterMineObject) - Method in class org.intermine.dataloader.SourcePriorityComparator
Compares two objects.
compare(Path, Path) - Method in class org.intermine.pathquery.PathLengthComparator
Compare paths by number elements they contain, shortest paths come first.
compare(AbstractTable, AbstractTable) - Method in class org.intermine.sql.precompute.QueryOptimiser.AbstractTableComparator
Compare two AbstractTables using equalsIgnoreAlias().
compare(AbstractConstraint) - Method in class org.intermine.sql.query.AbstractConstraint
Compare this AbstractConstraint with another, ignoring aliases in member fields and tables.
compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractConstraint
Compare this AbstractConstraint with another, ignoring aliases in member fields and tables.
compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
Compare the value of this AbstractValue with another.
compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Constant
Compare this Constant to another AbstractValue.
compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Constraint
Compare this Constraint with another AbstractConstraint, ignoring aliases in member fields and tables.
compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.ConstraintSet
Compare this ConstraintSet with another AbstractConstraint, ignoring aliases in member fields and tables.
compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Field
Compare this field to another AbstractValue.
compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Function
Compare the value of this AbstractValue with another.
compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.InListConstraint
Compare this InListConstraint with another AbstractConstraint, ignoring aliases in member fields and tables.
compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.NotConstraint
Compare this NotConstraint with another AbstractConstraint, ignoring aliases in member fields and tables.
compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.OrderDescending
Compare the value of this AbstractValue with another.
compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.SubQueryConstraint
Compare this SubQueryConstraint with another AbstractConstraint, ignoring aliases in member fields and tables.
compare(TemplateQuery, TemplateQuery) - Method in class org.intermine.template.TemplateComparator
Compare two TemplateQuery objects by title, falling back to name if the titles are identical.
compare(Object, Object) - Method in class org.intermine.util.NullFirstComparator
compare(Object, Object) - Method in class org.intermine.xml.full.RendererComparator
Compare two Class objects by name.
compareConstraints(Set<AbstractConstraint>, Set<AbstractConstraint>, Set<AbstractConstraint>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Compares 2 sets of AbstractConstraints
compareConstraints(Set<AbstractConstraint>, Set<AbstractConstraint>, Set<AbstractConstraint>, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Compares 2 sets of AbstractConstraints
comparesActualToExpected() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
compareSelectLists(List<SelectValue>, List<SelectValue>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Compares two Lists of SelectValues, and returns true if all the items in the first List are present in the second List, ignoring the SelectValue alias.
compareTo(GenomicRegion) - Method in class org.intermine.bio.web.model.GenomicRegion
 
compareTo(ClassDescriptor) - Method in class org.intermine.metadata.ClassDescriptor
compareTo(ParallelPrecomputer.Job) - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer.Job
compareTo(PrecomputedTable) - Method in class org.intermine.sql.precompute.PrecomputedTable
Implements Comparable's method, so we can put PrecomputedTable objects into SortedMaps.
compareTo(Row) - Method in class org.intermine.sql.writebatch.Row
compareTo(SummaryPath) - Method in class org.intermine.web.logic.querybuilder.SummaryPath
compareTo(Item) - Method in class org.intermine.xml.full.Item
Compare items first by class, then by identifier, intended for creating ordered output files.
complete - Variable in class org.intermine.objectstore.query.ResultsInfo
 
complete - Variable in class org.intermine.sql.query.ExplainResult
 
completelyFalse(Constraint) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Returns true if this constraint is always false, regardless of row values.
CompletelyFalseException - Exception in org.intermine.objectstore.intermine
Exception thrown if a Constraint is deemed to be completely false.
CompletelyFalseException() - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException
Constructor.
CompletelyFalseException(String) - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException
Constructor.
CompletelyFalseException(Throwable) - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException
Constructor.
CompletelyFalseException(String, Throwable) - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException
Constructor.
completelyTrue(Constraint) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Returns true if this constraint is always true, regardless of row values.
ComplexDisplayer - Class in org.intermine.bio.web.displayer
Displayer for gene/protein interactions using complex viewer
ComplexDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.ComplexDisplayer
Construct with config and the InterMineAPI.
compose(F<B, C>) - Method in class org.intermine.webservice.server.core.F
Compose two functions f and g producing a function h such that h(x) = f(g(x)).
composeClass(Class<?>...) - Static method in class org.intermine.util.DynamicUtil
Return the Class for the array of Class objects.
composeClass(Set<Class<?>>) - Static method in class org.intermine.util.DynamicUtil
Return the Class for a set of Class objects.
composeDescriptiveClass(Class<?>...) - Static method in class org.intermine.util.DynamicUtil
Return the Class for the array of Class objects.
COMPUTE_TOTAL_COUNT_PARAMETER - Static variable in class org.intermine.webservice.server.query.result.QueryResultRequestParser
Compute total count parameter name.
con - Variable in class org.intermine.sql.logging.DatabaseWriter
 
con - Variable in class org.intermine.sql.precompute.BestQueryExplainer
 
con - Variable in class org.intermine.sql.query.NotConstraint
 
con - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
config - Variable in class org.intermine.web.displayer.ReportDisplayer
 
config - Variable in class org.intermine.web.logic.widget.Widget
 
Config - Class in org.intermine.webservice.server.jbrowse
Provide standard JBrowse configuration files (trackList.json and refSeqs.json) that are required to run a JBrowse instance.
Config(InterMineAPI) - Constructor for class org.intermine.webservice.server.jbrowse.Config
Build a new instance with the injected API
ConfigAction - Class in org.intermine.bio.chado.config
A class that represents an action while processing synonyms, dbxrefs, etc.
ConfigAction() - Constructor for class org.intermine.bio.chado.config.ConfigAction
 
configAttr - Variable in class org.intermine.bio.dataconversion.GFF3Converter
 
configAttrClass - Variable in class org.intermine.bio.dataconversion.GFF3Converter
 
configExclude - Variable in class org.intermine.bio.dataconversion.GFF3Converter
 
configFileName - Variable in class org.intermine.task.SummariseObjectStoreTask
 
configTerm - Variable in class org.intermine.bio.dataconversion.GFF3Converter
 
ConfigurableMine - Interface in org.intermine.api.mines
A sub-interface of Mine to encapsulate the mutable elements of the interface, and not expose them the the consumer.
ConfigurableWebServiceServlet - Class in org.intermine.webservice.server.core
A servlet that can be configured entirely in XML.
ConfigurableWebServiceServlet() - Constructor for class org.intermine.webservice.server.core.ConfigurableWebServiceServlet
 
ConfigurationException - Exception in org.intermine.api.mines
An error caused when trying to configure something.
ConfigurationException(String) - Constructor for exception org.intermine.api.mines.ConfigurationException
Construct an exception with a message.
configure(Properties) - Method in interface org.intermine.api.mines.ConfigurableMine
Configure this mine with a the properties provided.
configure(Properties) - Method in class org.intermine.api.mines.HttpRequester
 
configure(Properties) - Method in class org.intermine.api.mines.LocalMine
 
configure(Properties) - Method in interface org.intermine.api.mines.MineRequester
Accept configuration provided in the form of properties.
configure(Properties) - Method in class org.intermine.api.mines.RemoteMine
 
configure(Properties) - Method in class org.intermine.sql.Database
Configures a datasource from a Properties object
configureDagTerm(Map<?, ?>) - Method in class org.intermine.bio.ontology.OboParser
Configure dag terms with values from one entry.
configureDynamicAttributes(Object) - Method in class org.intermine.task.DynamicAttributeTask
Look at set methods on a target object and lookup values in project properties.
configureItem(String, Item, OboTerm) - Method in class org.intermine.bio.dataconversion.OboConverter
Set up attributes and references for the Item created from a DagTerm.
configureSynonymItem(OboTermSynonym, Item, OboTerm) - Method in class org.intermine.bio.dataconversion.OboConverter
Set up attributes and references for the Item created from a DagTermSynonym.
conn - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
conn - Variable in class org.intermine.sql.precompute.PrecomputedTableManager
 
connect() - Method in class org.intermine.webservice.client.util.HttpConnection
Opens connection.
connection - Variable in class org.intermine.api.tracker.TrackerDelegate
 
connection - Variable in class org.intermine.api.tracker.xml.TrackHandler
 
connectionTakenBy - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
connInUse - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
cons - Variable in class org.intermine.sql.query.ConstraintSet
 
ConsistentSet<E> - Class in org.intermine.util
A Set that allows for its member objects to be changed whilst still belonging to the set.
ConsistentSet() - Constructor for class org.intermine.util.ConsistentSet
Constructor.
Constant - Class in org.intermine.sql.query
A representation of a constant value in an SQL query.
Constant(String) - Constructor for class org.intermine.sql.query.Constant
Constructor for this Constant object.
constant(B) - Static method in class org.intermine.webservice.server.core.F
Construct a constant function that discards its input and always returns the same value.
Constants - Class in org.intermine.api.config
A single constant.
Constants - Class in org.intermine.bio.util
 
Constants - Class in org.intermine.web.logic
Container for ServletContext and Session attribute names used by the webapp
Constraint - Class in org.intermine.objectstore.query
Abstract reperesentation of a query constraint.
Constraint() - Constructor for class org.intermine.objectstore.query.Constraint
 
Constraint - Class in org.intermine.sql.query
A representation of a normal constraint, comparing two AbstractValue objects.
Constraint(AbstractValue, int, AbstractValue) - Constructor for class org.intermine.sql.query.Constraint
Constructor for a Constraint object.
constraintAttributes - Variable in class org.intermine.pathquery.PathQueryHandler
 
constraintCode - Variable in class org.intermine.pathquery.PathQueryHandler
 
constraintDescriptions - Variable in class org.intermine.template.TemplateQuery
Descriptions of constraints
ConstraintHelper - Class in org.intermine.objectstore.query
Static methods to create Lists of Constraint objects in a query and Constraints in a query relating to a given QueryClass, plus helper methods for dealing with Constraints.
ConstraintInput - Class in org.intermine.web.logic.template
Simple object that carries constraint values for other processing.
ConstraintInput(String, String, String, ConstraintOp, String, List<String>, String) - Constructor for class org.intermine.web.logic.template.ConstraintInput
ConstraintLoad constructor.
constraintLogic - Variable in class org.intermine.pathquery.PathQueryHandler
 
ConstraintOp - Class in org.intermine.metadata
Operations used in building constraints.
ConstraintOptions - Class in org.intermine.api.query.range
A bundle of options consumed by the AbstractHelper when generating constraint sets for a set of ranges.
ConstraintOptions(ConstraintOp, ConstraintOp, ConstraintOp, ConstraintOp) - Constructor for class org.intermine.api.query.range.ConstraintOptions
Construct a new set of constraint options.
ConstraintOptions(ConstraintOp, ConstraintOp, ConstraintOp, ConstraintOp, String, String) - Constructor for class org.intermine.api.query.range.ConstraintOptions
Construct a new set of constraint options.
constraintPath - Variable in class org.intermine.pathquery.PathQueryHandler
 
constraints - Variable in class org.intermine.objectstore.query.ConstraintSet
 
Constraints - Class in org.intermine.pathquery
Builds constraints for the PathQuery.
ConstraintSet - Class in org.intermine.objectstore.query
Groups a series of Constraints together.
ConstraintSet(ConstraintOp) - Constructor for class org.intermine.objectstore.query.ConstraintSet
Construct empty ConstraintSet
ConstraintSet - Class in org.intermine.sql.query
A representation of a set of constraints ORed together.
ConstraintSet() - Constructor for class org.intermine.sql.query.ConstraintSet
Constructor for a ConstraintSet object.
constraintSetToString(SqlGenerator.State, StringBuffer, ConstraintSet, Query, DatabaseSchema, int, boolean) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a ConstraintSet object into a String suitable for putting in an SQL query.
constraintSwitchOffAbility - Variable in class org.intermine.template.TemplateQuery
Configuration for switch-off-ability of constraints
constraintToString(SqlGenerator.State, StringBuffer, Constraint, Query, DatabaseSchema, int, boolean) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a Constraint object into a String suitable for putting in an SQL query.
constraintToString(Query, Constraint, List<Object>) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Converts a Constraint into a String.
ConstraintTraverseAction - Interface in org.intermine.objectstore.query
ConstraintTraverseActions are passed to the traverseConstraints() method.
ConstraintValueParser - Class in org.intermine.pathquery
Parser for parsing constraint value.
constraintValues - Variable in class org.intermine.pathquery.PathQueryHandler
 
ConstraintWithBag - Interface in org.intermine.objectstore.query
Common interface for BagConstraint and MultipleInBagConstraint defining the getBag() method.
constructQueries(boolean, ObjectStore, String, String) - Static method in class org.intermine.task.PrecomputeTask
Create queries for given path.
constructQuery(Model, String) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil
Construct an objectstore query represented by the given path.
ContactAction - Class in org.intermine.web.struts
Action handles submission of user feedback form.
ContactAction() - Constructor for class org.intermine.web.struts.ContactAction
 
ContactForm - Class in org.intermine.web.struts
Form bean representing feedback form.
ContactForm() - Constructor for class org.intermine.web.struts.ContactForm
Creates a new instance of ContactForm
CONTAINS - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument contains the second
contains(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to contain a value.
contains(Object) - Method in class org.intermine.util.AlwaysSet
contains(int) - Method in class org.intermine.util.IntPresentSet
Returns whether the given int is present in this set.
contains(Integer) - Method in class org.intermine.util.IntPresentSet
Returns whether the given Integer is present in this set.
contains(Collection<?>, Object) - Static method in class org.intermine.web.logic.WebUtil
So we can test set membership in JSPs.
contains(Object) - Method in class org.intermine.webservice.client.lists.ItemList
 
contains(Object) - Method in class org.intermine.webservice.client.results.ResultRowList
 
contains(ItemList, Item...) - Method in class org.intermine.webservice.client.services.ListService
Report whether the given list contains all the items in the supplied array.
containsAll(Collection<?>) - Method in class org.intermine.util.AlwaysSet
containsAll(Collection<?>) - Method in class org.intermine.util.PseudoSet
containsAll(Collection) - Method in class org.intermine.webservice.client.lists.ItemList
 
containsAll(Collection<?>) - Method in class org.intermine.webservice.client.results.ResultRowList
 
containsCollections() - Method in class org.intermine.pathquery.Path
Return true if and only if any part of the path is a collection.
ContainsConstraint - Class in org.intermine.objectstore.query
Constrain whether a QueryClass is member of a QueryReference or not.
ContainsConstraint(QueryReference, ConstraintOp, QueryClass) - Constructor for class org.intermine.objectstore.query.ContainsConstraint
Constructor for ContainsConstraint.
ContainsConstraint(QueryReference, ConstraintOp, InterMineObject) - Constructor for class org.intermine.objectstore.query.ContainsConstraint
Constructor for ContainsConstraint.
ContainsConstraint(QueryReference, ConstraintOp) - Constructor for class org.intermine.objectstore.query.ContainsConstraint
Constructor for ContainsConstraint, constrain a reference/collection to be NULL/ NOT NULL
containsConstraintToString(SqlGenerator.State, StringBuffer, ContainsConstraint, Query, DatabaseSchema, int, boolean) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a ContainsConstraint object into a String suitable for putting in an SQL query.
containsHeaders(String, StringBuffer) - Method in class org.intermine.web.struts.ContactForm
Check part of the message for injected headers.
containsKey(Object) - Method in class org.intermine.util.AlwaysMap
containsKey(Object) - Method in class org.intermine.util.IdentityMap
containsKey(Object) - Method in class org.intermine.util.ReferenceMap
containsKey(Object) - Method in class org.intermine.web.logic.results.ReportObjectFactory
Always returns true because get always returns an Object.
containsKey(Map<?, ?>, Object) - Static method in class org.intermine.web.logic.WebUtil
So we can test map membership in JSPs.
containsReferences() - Method in class org.intermine.pathquery.Path
Return true if and only if any part of the path is a reference.
containsValue(Object) - Method in class org.intermine.util.AlwaysMap
containsValue(Object) - Method in class org.intermine.util.IdentityMap
containsValue(Object) - Method in class org.intermine.util.ReferenceMap
ContentType - Enum in org.intermine.api.mines
An enumeration of the content-types we know about.
ContentType - Class in org.intermine.webservice.client.core
Simple class wrapping content type information.
ContextNotInitialisedException - Exception in org.intermine.web.context
An error thrown when the InterMineContext object has not been initialised.
ContextNotInitialisedException(String) - Constructor for exception org.intermine.web.context.ContextNotInitialisedException
 
convert(ResultSet, Query, ObjectStoreInterMineImpl, Connection, Map<Object, Integer>, boolean, ExtraQueryTime, Set<PrecomputedTable>, OptimiserCache) - Static method in class org.intermine.objectstore.intermine.ResultsConverter
Method to convert from SQL results to InterMine object-based results.
convert(List<ResultElement>, Collection<Path>, Collection<Path>) - Method in class org.intermine.web.logic.export.ResultElementConverter
Converts data from ResultElement to Objects.
convert(Item) - Static method in class org.intermine.xml.full.ItemHelper
Convert an XML item to a data model one
convert(ReferenceList) - Static method in class org.intermine.xml.full.ItemHelper
Convert a xml ReferenceList to a fulldata ReferenceList that can then be stored with ItemWriter
convert(Reference) - Static method in class org.intermine.xml.full.ItemHelper
Convert a xml Reference to a fulldata Reference that can then be stored with ItemWriter
convert(Attribute) - Static method in class org.intermine.xml.full.ItemHelper
Convert a xml Attribute to a fulldata Attribute that can then be stored with ItemWriter
convert(Item) - Static method in class org.intermine.xml.full.ItemHelper
Convert a data model item to an XML one
ConvertBagController - Class in org.intermine.web.struts
 
ConvertBagController() - Constructor for class org.intermine.web.struts.ConvertBagController
 
ConvertedObjectPair - Class in org.intermine.api.bag
A class to represent the mapping between an object before type conversion and the converted object.
ConvertedObjectPair(InterMineObject, InterMineObject) - Constructor for class org.intermine.api.bag.ConvertedObjectPair
Create a new ConvertedObjectPair.
converter - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler
 
converter - Variable in class org.intermine.bio.task.GFF3ConverterTask
 
ConverterTask - Class in org.intermine.task
Task superclass for invoking converters.
ConverterTask() - Constructor for class org.intermine.task.ConverterTask
 
convertResultMapToHTML(Map<GenomicRegion, List<List<String>>>, Map<GenomicRegion, Map<String, Integer>>, List<GenomicRegion>, int, int, HttpSession) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Convert result map to HTML string.
convertToClasses(Set<String>) - Static method in class org.intermine.util.DynamicUtil
Convert a set of interface names to a set of Class objects
copyField(FastPathObject, FastPathObject, Source, Source, FieldDescriptor, int) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Copies the value of the field given from the source object into the destination object.
copyInterMineObject(O) - Static method in class org.intermine.bio.postprocess.PostProcessUtil
Create a copy of given InterMineObject with *no* id set and copies of collections
correction - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
CorrectionCoefficient - Interface in org.intermine.web.logic.widget
An Interface which defines when/how a correction coefficient can be applied to the results obtained by a enrichment widget
correctOfficialName(String, String) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Unify variations on similar official names.
count(PathQuery) - Method in class org.intermine.api.query.QueryExecutor
Take a query and return the results row count.
count - Variable in class org.intermine.dataconversion.FullXmlConverter
 
count(Query, Map<Object, Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Counts the number of rows the query will produce
count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Counts the number of rows the query will produce
count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Counts the number of rows the query will produce
count(Query, Map<Object, Integer>) - Method in interface org.intermine.objectstore.ObjectStore
Counts the number of rows the query will produce
count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Counts the number of rows the query will produce
COUNT - Static variable in class org.intermine.objectstore.query.QueryFunction
Count rows
count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Counts the number of rows the query will produce
count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Counts the number of rows the query will produce
COUNT - Static variable in class org.intermine.sql.query.Function
COUNT(*) aggregate function - takes no operands.
countOccurances(String, String) - Static method in class org.intermine.metadata.StringUtil
Returns the number of occurances of str in target
CountProcessor - Class in org.intermine.webservice.server.core
A class that processes counts.
CountProcessor() - Constructor for class org.intermine.webservice.server.core.CountProcessor
Constructor
countResolutions(String, String) - Method in class org.intermine.bio.dataconversion.DoNothingIdResolver
 
countResolutions(String, String, String) - Method in class org.intermine.bio.dataconversion.IdResolver
Return the count of matching primary identifiers for a particular identifier
countResolutions(String, String) - Method in class org.intermine.bio.dataconversion.IdResolver
Return the count of matching primary identifiers for a particular identifier
CountTableController - Class in org.intermine.web.struts
Start a count in a separate thread of the number of rows in the PagedTable given by the "resultsTable" request attribute.
CountTableController() - Constructor for class org.intermine.web.struts.CountTableController
 
countWithConnection(Connection, Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Counts the results in a query, given a Connection.
create() - Method in class org.intermine.bio.postprocess.CreateLocationOverlapIndex
Create an int4range or bioseg index on the start and end columns of the of the location table.
create(Class<? extends FastPathObject>, Class<?>[]) - Static method in class org.intermine.util.DynamicBean
Create a DynamicBean
CREATE_SYNONYM_ACTION - Static variable in class org.intermine.bio.dataconversion.SequenceProcessor
An action that makes a synonym.
CreateAccountAction - Class in org.intermine.web.struts
 
CreateAccountAction() - Constructor for class org.intermine.web.struts.CreateAccountAction
 
CreateAccountForm - Class in org.intermine.web.struts
Form bean to represent the inputs to create a new user account
CreateAccountForm() - Constructor for class org.intermine.web.struts.CreateAccountForm
 
createAllelesTempTable(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Create a temporary table of allele feature_ids.
createAnonymousProfile() - Method in class org.intermine.api.profile.ProfileManager
Create a profile not tied to an entry in the user db.
createAttributePath(String[], int) - Method in class org.intermine.web.logic.widget.WidgetLdr
Return the path of the attribute at the the position index in the paths given in input without reference to subclass.
createBag(String, String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.Profile
Create a bag and save it to the userprofile database.
createBag(String, String, String, Map) - Method in class org.intermine.api.util.AnonProfile
 
createBagFromPathQuery(PathQuery, String, String, String, Profile, InterMineAPI) - Static method in class org.intermine.web.logic.bag.BagHelper
Create a bag for the given profile and bag name from a PathQuery.
createBagTable(Database, Connection, String, Collection<?>, Class<?>) - Static method in class org.intermine.sql.DatabaseUtil
Create a new table the holds the contents of the given Collection (bag).
createBagValuesTables(Connection) - Static method in class org.intermine.sql.DatabaseUtil
Create the table 'bagvalues' containing the values of the key field objects contained in a bag and an extra values
createBasicLocalProfile(String, String, String) - Method in class org.intermine.api.profile.ProfileManager
Create a new Profile with the given username, password and api-key.
createClassFindingQuery(Model, String) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil
Takes a String representation of a query (a path), and creates a query.
createClasspath() - Method in class org.intermine.task.ReadResourceTask
Create an empty Path.
createClob() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Creates a new empty Clob that is valid for this ObjectStore.
createClob() - Method in interface org.intermine.objectstore.ObjectStore
Creates a new empty Clob that is valid for this ObjectStore.
createClob() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Creates a new empty Clob that is valid for this ObjectStore.
createClob() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Creates a new empty Clob that is valid for this ObjectStore.
CreateCollectionAction - Class in org.intermine.bio.chado.config
An action that creates a collection of objects from value.
CreateCollectionAction(String, String, String, boolean) - Constructor for class org.intermine.bio.chado.config.CreateCollectionAction
Create a new CreateCollectionAction object.
createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in class org.intermine.api.query.range.AbstractHelper
Extending classes may with to override this method if they need to adjust the main constraint set in some way, such as adding an extra constraint.
createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in class org.intermine.api.query.range.IntHelper
 
createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in class org.intermine.api.query.range.StringHelper
 
createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in interface org.intermine.api.query.RangeHelper
 
createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in class org.intermine.bio.query.range.ChromosomeLocationHelper
 
createConstraintStructure(LogicExpression, ConstraintSet, Map<String, Constraint>) - Static method in class org.intermine.api.query.MainHelper
Given a LogicExpression, a Map from codes to Constraint objects, and a ConstraintSet to put it all in, construct a tree of ConstraintSets that reflects the expression.
createConstraintStructure(LogicExpression.Node, ConstraintSet, Map<String, Constraint>) - Static method in class org.intermine.api.query.MainHelper
Given a LogicExpression.Node, a Map from codes to Constraint objects, and a ConstraintSet to put it all in, construct a tree of ConstraintSets that reflects the expression.
createCrossReference(String, String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter
Create a new CrossReference.
createCrossReference(String, String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioFileConverter
Create a new CrossReference.
createDefaultBagQuery(String, BagQueryConfig, Model, Map<String, List<FieldDescriptor>>, Collection<String>) - Static method in class org.intermine.api.bag.BagQueryHelper
Create a BagQuery that constrains the class key fields of the given type.
createDefaultFeedbackMsg(HttpServletRequest) - Method in class org.intermine.web.struts.ContactForm
Create the default feedback messages.
createFeatureTempTable(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Create a temporary table containing only the features that interest us.
createFlankingFeatures() - Method in class org.intermine.bio.postprocess.CreateFlankingRegions
Iterate over genes in database and create flanking regions.
CreateFlankingRegions - Class in org.intermine.bio.postprocess
Create features to represent flanking regions of configurable distance either side of gene features.
CreateFlankingRegions(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.CreateFlankingRegions
Create a new CreateFlankingRegions object that will operate on the given ObjectStoreWriter.
createFromDb(Set<String>, Database) - Method in class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory
 
createFromDb(Database) - Method in class org.intermine.bio.dataconversion.IdResolverFactory
Read IdResolver contents from a database.
createFromDb(String, Database) - Method in class org.intermine.bio.dataconversion.IdResolverFactory
Read IdResolver contents from a database.
createFromDb(Set<String>, Database) - Method in class org.intermine.bio.dataconversion.IdResolverFactory
Read IdResolver contents from a database.
createFromDb(Database) - Method in class org.intermine.bio.dataconversion.OntologyIdResolverFactory
 
createFromDb(Database) - Method in class org.intermine.bio.dataconversion.WormBaseIdResolverFactory
 
createFromFile(File) - Method in class org.intermine.bio.dataconversion.EnsemblIdResolverFactory
Populate the ID resolver from a tab delimited file
createFromFile(File, Set<String>) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
Populate the ID resolver from a tab delimited file
createFromFile(File) - Method in class org.intermine.bio.dataconversion.HgncIdResolverFactory
Populate the ID resolver from a tab delimited file
createFromFile(File) - Method in class org.intermine.bio.dataconversion.HumanIdResolverFactory
Populate the ID resolver from a tab delimited file
createFromFile(File) - Method in class org.intermine.bio.dataconversion.MgiIdentifiersResolverFactory
Populate the ID resolver from a tab delimited file
createFromFile(File) - Method in class org.intermine.bio.dataconversion.RgdIdentifiersResolverFactory
Populate the ID resolver from a tab delimited file
createFromFile(File) - Method in class org.intermine.bio.dataconversion.ZfinIdentifiersResolverFactory
Populate the ID resolver from a tab delimited file
createFromWb2NcbiFile(File) - Method in class org.intermine.bio.dataconversion.WormBaseIdResolverFactory
Populate the ID resolver from a tab delimited file
createFromWormIdFile(File) - Method in class org.intermine.bio.dataconversion.WormBaseIdResolverFactory
Populate the ID resolver from a tab delimited file
createGenomicRegionsFromString(Collection<String>, String, Integer, Boolean) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchUtil
Create a list of GenomicRegion objects from a collection of region strings
createGetRequest(String, ContentType) - Method in class org.intermine.webservice.client.core.Service
Creates GET request.
createIdResolver() - Method in class org.intermine.bio.dataconversion.DoNothingIdResolverFactory
 
createIdResolver() - Method in class org.intermine.bio.dataconversion.EnsemblIdResolverFactory
 
createIdResolver(String) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
Build an IdResolver from Entrez Gene gene_info file
createIdResolver(Set<String>) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
Build an IdResolver from Entrez Gene gene_info file.
createIdResolver() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
 
createIdResolver() - Method in class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory
Build an IdResolver for FlyBase by accessing a FlyBase chado database.
createIdResolver() - Method in class org.intermine.bio.dataconversion.HgncIdResolverFactory
Build an IdResolver for HGNC.
createIdResolver() - Method in class org.intermine.bio.dataconversion.HumanIdResolverFactory
 
createIdResolver() - Method in class org.intermine.bio.dataconversion.IdResolverFactory
Create and IdResolver from source information.
createIdResolver() - Method in class org.intermine.bio.dataconversion.MgiIdentifiersResolverFactory
 
createIdResolver() - Method in class org.intermine.bio.dataconversion.MockIdResolverFactory
 
createIdResolver() - Method in class org.intermine.bio.dataconversion.OntologyIdResolverFactory
Build an IdResolver.
createIdResolver() - Method in class org.intermine.bio.dataconversion.RgdIdentifiersResolverFactory
 
createIdResolver() - Method in class org.intermine.bio.dataconversion.WormBaseIdResolverFactory
Build an IdResolver for WormBase by accessing a WormBase chado database.
createIdResolver() - Method in class org.intermine.bio.dataconversion.ZfinIdentifiersResolverFactory
Build an IdResolver from Entrez Gene gene_info file
createIndex(Connection, String, IndexStatement, int) - Method in class org.intermine.task.CreateIndexesTask
Create an named index on the specified columns of a table.
CreateIndexesTask - Class in org.intermine.task
Task to create indexes on a database holding objects conforming to a given model by reading that model's primary key configuration information.
CreateIndexesTask() - Constructor for class org.intermine.task.CreateIndexesTask
 
createInsertionTempTable(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Create a temporary table from pairs of insertions (eg.
createIntergenicRegionFeatures() - Method in class org.intermine.bio.postprocess.IntergenicRegionUtil
Create IntergenicRegion objects
createIntergenicRegionFeatures(Set<Location>, Map<Integer, Set<Gene>>, Integer) - Method in class org.intermine.bio.postprocess.IntergenicRegionUtil
Return an iterator over a Set of IntergenicRegion objects that don't overlap the Locations in the locationSet argument.
createIntronFeatures() - Method in class org.intermine.bio.postprocess.IntronUtil
Create Intron objects
createIntronFeatures(Set<Location>, SequenceFeature, Location, Gene) - Method in class org.intermine.bio.postprocess.IntronUtil
Return a set of Intron objects that don't overlap the Locations in the locationSet argument.
createIsoformEntry(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
no: features gene items, just identifiers - for memory reasons sequence, length, molecular weight, md5checksum components - per rachel isoforms - per mike
createItem(GFF3Converter) - Method in class org.intermine.bio.dataconversion.GFF3SeqHandler
Create the sequence item from the converter.
createItem(String) - Method in class org.intermine.dataconversion.DataConverter
Create item for the given class name.
createKeyStore() - Method in class org.intermine.web.task.KeyStoreTask
Create and return the configured key-store.
createList(Query) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Converts a constraint from a query into a List of Constraint objects.
createList(Query, FromElement) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Return a List of Constraint objects that relate to the given FromElement.
createList(ListService.ListCreationInfo) - Method in class org.intermine.webservice.client.services.ListService
Create a new list on the server by specifying its content.
createLocatedGenesTempTable(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Create a temporary table containing the ids of the located genes.
CreateLocationOverlapIndex - Class in org.intermine.bio.postprocess
Create an index on the location table to be used for range queries.
CreateLocationOverlapIndex(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.CreateLocationOverlapIndex
Construct a new CreateLocationRange
createLocations(GFF3Record) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Return true if Location objects should be made for all features (which is the default).
createNew(String) - Static method in class org.intermine.metadata.TypeUtil
Encapsulate the logic of requesting an object of a class named name where that class has a default no-arguments constructor.
createNewProfile(String, String) - Method in class org.intermine.api.profile.ProfileManager
Create a new profile in db with username and password given in input
createObject(String) - Method in class org.intermine.dataloader.DirectDataLoader
Create a new object of the given class name and give it a unique ID.
createObject(Class<C>) - Method in class org.intermine.dataloader.DirectDataLoader
Create a new object of the given class and give it a unique ID.
createObject(Set<? extends Class<?>>) - Static method in class org.intermine.util.DynamicUtil
Create a DynamicBean from a Set of Class objects
createObject(Class<C>) - Static method in class org.intermine.util.DynamicUtil
Create a new object given a class (not an interface).
createObjectStoreBag() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Returns a new empty ObjectStoreBag for this ObjectStore, delegate to internal ObjectStoreWriter.
createObjectStoreBag() - Method in interface org.intermine.objectstore.ObjectStore
Returns a new empty ObjectStoreBag object that is valid for this ObjectStore.
createObjectStoreBag() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Creates a new empty ObjectStoreBag object that is valid for this ObjectStore.
createObjectStoreBag() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Returns a new empty ObjectStoreBag object that is valid for this ObjectStore.
createOverlapRelations(List<String>, boolean) - Method in class org.intermine.bio.postprocess.CalculateLocations
Deprecated.
You should be using the create-overlap-view task instead
createOverlaps(ObjectStore, SequenceFeature, List<?>, boolean, ObjectStoreWriter, Map<String, Integer>) - Static method in class org.intermine.bio.postprocess.OverlapUtil
Creates OverlapRelations for overlapping SequenceFeature objects that are located on the given subject (generally a Chromosome).
createPasswordChangeToken(String) - Method in class org.intermine.api.profile.ProfileManager
Creates a password change token assigned to the given username that will expire after a day.
createPathConstraint(PathConstraint, String) - Method in class org.intermine.api.profile.PathQueryUpdate
Create a pathconstraint with the same operator and value of path contraint given in input and with the path given in input
createPathQuery() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
Returns the pathquery based on the views set in config file and the bag constraint Executed when the user selects any item in the matches column in the enrichment widget.
createPathQuery(String) - Method in class org.intermine.webservice.client.services.QueryService
Constructs a PathQuery from its XML representation.
createPathQueryView(ObjectStore, WidgetConfig) - Method in class org.intermine.web.logic.widget.Widget
Create a pathquery having a view composed by all items set in the view attribute in the config file
createPKQueriesForClass(InterMineObject, Source, boolean, ClassDescriptor) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Generates a query that searches for all objects in the database equivalent to a given example object, considering only one of it's classes.
createPKQueriesForClass(InterMineObject, Source, boolean, ClassDescriptor) - Method in interface org.intermine.dataloader.EquivalentObjectFetcher
Generates a query that searches for all objects in the database equivalent to a given example object, considering only one of it's classes.
createPKQueriesForClass(InterMineObject, Source, boolean, ClassDescriptor) - Method in class org.intermine.dataloader.HintingFetcher
Generates a query that searches for all objects in the database equivalent to a given example object, considering only one of it's classes.
createPKQuery(InterMineObject, Source, boolean) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Generates a query that searches for all objects in the database equivalent to a given example object according to the primary keys defined for the given source.
createPKQuery(InterMineObject, Source, boolean) - Method in interface org.intermine.dataloader.EquivalentObjectFetcher
Generates a query that searches for all objects in the database equivalent to a given example object according to the primary keys defined for the given source.
createPKQueryForPK(InterMineObject, boolean, ClassDescriptor, PrimaryKey, Source, Set<Query>) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Adds a Query to handle a primary key to a Set.
createPKQueryForPK(InterMineObject, boolean, ClassDescriptor, PrimaryKey, Source, Set<Query>) - Method in class org.intermine.dataloader.HintingFetcher
Adds a Query to handle a primary key to a Set.
createPostRequest(String, ContentType) - Method in class org.intermine.webservice.client.core.Service
Creates POST request.
createProfile(Profile) - Method in class org.intermine.api.profile.ProfileManager
Creates a profile in the userprofile database.
createProfileWithoutBags(Profile) - Method in class org.intermine.api.profile.ProfileManager
Creates a profile in the userprofile database without adding bag.
CreatePropertiesFile - Class in org.intermine.task
 
CreatePropertiesFile() - Constructor for class org.intermine.task.CreatePropertiesFile
 
createQueries(GenomicRegionSearchListInput.GenomicRegionSearchInfo) - Method in class org.intermine.bio.webservice.GenomicRegionSearchService
Create the queries used to run the genomic region search.
createQueryFieldByPath(String, Query, boolean) - Method in class org.intermine.web.logic.widget.WidgetLdr
Create a queryField starting from the path given in input and add the contain constraints between all the queryclass composing the path.
createQueryForExampleObject(Model, InterMineObject, Set<String>) - Static method in class org.intermine.objectstore.query.QueryCreator
Generates a query that searches for all objects in the database that have the fieldnames set to the values in the object.
createQueryForId(Integer, Class<? extends InterMineObject>) - Static method in class org.intermine.objectstore.query.QueryCreator
Create a query that will retrieve an object from the objectstore, given an ID.
createQueryForIds(Collection<Integer>, Class<? extends InterMineObject>) - Static method in class org.intermine.objectstore.query.QueryCreator
Create a query that will retrieve all objects with the given IDs from the objectstore.
createQueryForQueryNodeValues(Query, QueryNode) - Static method in class org.intermine.objectstore.query.QueryCreator
Create a query that will list the options for a particular field or class in a query, given the existing constraints For example: Original query: SELECT c, d FROM Company AS c, Department AS d WHERE c.departments CONTAINS d AND c.name LIKE 'A%' We want to know the possible department names are that we might want to constrain Returned query: SELECT DISTINCT d.name FROM Company AS c, Department AS d WHERE c.departments CONTAINS d AND c.name LIKE 'A%'
createQueryList() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
To prepare queries for genomic regions
createQueryList(Collection<GenomicRegion>, int, String, Set<Class<?>>) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchUtil
Create a list of queries from user regions.
createRAMIndex(String) - Method in class org.intermine.web.autocompletion.AutoCompleter
create the RAMIndex for the search engine
CreateReferences - Class in org.intermine.bio.postprocess
Fill in additional references/collections in genomic model
CreateReferences(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.CreateReferences
Construct with an ObjectStoreWriter, read and write from same ObjectStore
createRegionListQueries(Collection<GenomicRegion>, int, Map<String, ChromosomeInfo>, String, Set<Class<?>>) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchUtil
Create a list of queries from user regions.
CreateSearchIndexTask - Class in org.intermine.web.task
Create a the Lucene keyword search index for a mine.
CreateSearchIndexTask() - Constructor for class org.intermine.web.task.CreateSearchIndexTask
 
createSignature() - Method in enum org.intermine.webservice.server.JWTBuilder.Algorithm
 
createSimpleObject(Class<C>) - Method in class org.intermine.dataloader.DirectDataLoader
Create a 'simple object' which doesn't inherit from InterMineObject and doesn't have an id.
createSingletons() - Method in class org.intermine.bio.chado.config.CreateCollectionAction
If true, create only one object of class className with each possible fieldName; if false, multiple objects with the same value for fieldName might be created
createSituation - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
createSpanningLocations(String, String, String) - Method in class org.intermine.bio.postprocess.CalculateLocations
Create a Location that spans the locations of some child objects.
createSQLStatement(String, String) - Method in class org.intermine.sql.logging.DatabaseWriter
Creates an SQL String suitable for initialising a PreparedStatement
createSubFeatureIdTempTable(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Create a temporary table of all feature_ids for a given submission.
createSuperUser(String, String, String) - Method in class org.intermine.api.profile.ProfileManager
Create a super-user with the given username, password and API-key.
createSynonym(String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioDBConverter
Create a new Synonym.
createSynonym(String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter
Create a new Synonym.
createSynonym(Item, String, boolean) - Method in class org.intermine.bio.dataconversion.BioFileConverter
Create a new Synonym.
createSynonym(String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioFileConverter
Create a new Synonym.
createSynonym(FeatureData, String) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Call DataConverter.createSynonym(), store the Item then record in FeatureData that we've created it.
createSynonym(FeatureData, String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Call DataConverter.createSynonym(), store the Item then record in FeatureData that we've created it.
CreateSynonymAction - Class in org.intermine.bio.chado.config
An action that sets a Synonym.
CreateSynonymAction() - Constructor for class org.intermine.bio.chado.config.CreateSynonymAction
Make a synonym
CreateSynonymAction(Pattern) - Constructor for class org.intermine.bio.chado.config.CreateSynonymAction
Make a synonym and use the type from chado ("symbol", "identifier" etc.) as the Synonym type.
createTempBagTable(ConstraintWithBag) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates a temporary bag table for the given BagConstraint.
createTempBagTable(Connection, ConstraintWithBag, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates a temporary bag table for the given BagConstraint.
createTempBagTable(Connection, QueryClassBag, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates a temporary bag table for the given QueryClassBag.
createTempBagTables(Connection, Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Create temporary tables for use with Query that use bags.
CreateTemplateAction - Class in org.intermine.web.struts
Action to create a new TemplateQuery from current query.
CreateTemplateAction() - Constructor for class org.intermine.web.struts.CreateTemplateAction
 
createToken(Profile, int) - Method in class org.intermine.webservice.server.user.DeletionTokens
Create a new DeletionToken
createTrackerTable(Connection) - Method in class org.intermine.api.tracker.AbstractTracker
Create the table where the tracker saves data
createTrackerTable(Connection) - Method in interface org.intermine.api.tracker.Tracker
Create the table where the tracker saves data
createTrailLabel(InterMineObject, Model) - Static method in class org.intermine.web.struts.ObjectTrailController
Create trail element label.
createUtrRefs() - Method in class org.intermine.bio.postprocess.CreateReferences
Read the UTRs collection of MRNA then set the fivePrimeUTR and threePrimeUTR fields with the corresponding UTRs.
createView() - Method in class org.intermine.bio.postprocess.OverlapViewTask
Drop the sequencefeatureoverlappingfeatures table and replace it with a view that uses the bioseg type to calculate the overlaps.
createWithObjects(String, Item, String, String) - Method in class org.intermine.bio.dataconversion.GoConverter
Given the 'with' text from a gene_association entry parse for recognised identifier types and create Gene or Protein items accordingly.
CreationEvent - Class in org.intermine.api.search
A representation of a notification a web searchable object has been created.
CreationEvent(WebSearchable) - Constructor for class org.intermine.api.search.CreationEvent
Constructor.
CSVExportForm - Class in org.intermine.web.struts
A form to hold options for CSV and tab separated output.
CSVExportForm() - Constructor for class org.intermine.web.struts.CSVExportForm
 
CSVFormatter - Class in org.intermine.webservice.server.output
Formats data to comma separated data format.
CSVFormatter() - Constructor for class org.intermine.webservice.server.output.CSVFormatter
Construct a CSV formatter.
CSVHttpExporter - Class in org.intermine.web.logic.export.http
Exporter that exports table with results in comma separated format.
CSVHttpExporter() - Constructor for class org.intermine.web.logic.export.http.CSVHttpExporter
Constructor.
CSVRowFormatter - Class in org.intermine.web.logic.export.rowformatters
Row formatter formats line as comma separated strings.
CSVRowFormatter() - Constructor for class org.intermine.web.logic.export.rowformatters.CSVRowFormatter
Constructor.
CuratedProteinsDisplayer - Class in org.intermine.bio.web.displayer
 
CuratedProteinsDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.CuratedProteinsDisplayer
Construct with config and the InterMineAPI.
currentArray - Variable in class org.intermine.webservice.server.output.JSONResultsIterator
 
currentIterator - Variable in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator
 
currentIterator - Variable in class org.intermine.util.CombinedIterator
 
currentMap - Variable in class org.intermine.webservice.server.output.JSONResultsIterator
 
currentNodePath - Variable in class org.intermine.pathquery.PathQueryHandler
 
CurrentQueryAction - Class in org.intermine.web.struts
Action to display the query builder (if there is a current query) or redirect to project.sitePrefix.
CurrentQueryAction() - Constructor for class org.intermine.web.struts.CurrentQueryAction
 
CustomOAuthProvider - Class in org.intermine.web.struts.oauth2
A representation of an OAuth provider which has been configured entirely in web-properties.
CustomOAuthProvider(Properties, String) - Constructor for class org.intermine.web.struts.oauth2.CustomOAuthProvider
Construct a new provider.
CustomPrintWriter - Class in org.intermine.web.logic.export
Customized PrintWriter that terminates end of the lines with defined line separator.
CustomPrintWriter(OutputStream, String) - Constructor for class org.intermine.web.logic.export.CustomPrintWriter
Constructor.
CytoscapeNetworkDisplayer - Class in org.intermine.bio.web.displayer
Displayer for gene/protein interactions using cytoscape plugin
CytoscapeNetworkDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.CytoscapeNetworkDisplayer
Construct with config and the InterMineAPI.

D

dagFilename - Variable in class org.intermine.bio.dataconversion.OboConverter
 
Database - Class in org.intermine.sql
Class that represents a physical SQL database
Database() - Constructor for class org.intermine.sql.Database
No argument constructor for testing purposes
Database(Properties) - Constructor for class org.intermine.sql.Database
Constructs a Database object from a set of properties
database - Variable in class org.intermine.sql.precompute.PrecomputedTableManager
 
database - Variable in class org.intermine.task.AnalyseDbTask
 
database - Variable in class org.intermine.task.BuildDbTask
 
database - Variable in class org.intermine.task.GrantTask
 
database - Variable in class org.intermine.task.RetrieveMetadataTask
 
database - Variable in class org.intermine.task.StoreMetadataTask
 
databaseAlias - Variable in class org.intermine.task.BuildDbTask
 
databaseAltered(Set<Object>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Internal method called by the ObjectStoreWriter, to notify the ObjectStore that some of the data in the database has changed.
databaseAltered(Set<Object>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Internal method called by the ObjectStoreWriter, to notify the ObjectStore that some of the data in the database has changed.
DatabaseConnectionException - Exception in org.intermine.sql
Exception thrown on failing to object a database connection.
DatabaseConnectionException() - Constructor for exception org.intermine.sql.DatabaseConnectionException
Constructs an DatabaseConnectionException
DatabaseConnectionException(String) - Constructor for exception org.intermine.sql.DatabaseConnectionException
Constructs an ObjectStoreException with the specified detail message.
DatabaseConnectionException(Throwable) - Constructor for exception org.intermine.sql.DatabaseConnectionException
Constructs an ObjectStoreException with the specified nested throwable.
DatabaseConnectionException(String, Throwable) - Constructor for exception org.intermine.sql.DatabaseConnectionException
Constructs an ObjectStoreException with the specified detail message and nested throwable.
databaseEmpty() - Method in class org.intermine.dataloader.EquivalentObjectHints
Returns true if the database was empty at the start of the run.
DatabaseFactory - Class in org.intermine.sql
Creates Databases
databases - Static variable in class org.intermine.sql.DatabaseFactory
 
DatabaseSchema - Class in org.intermine.objectstore.intermine
An object that represents the mapping of a Model onto a relational database.
DatabaseSchema(Model, List<ClassDescriptor>, boolean, Set<String>, int, boolean, boolean) - Constructor for class org.intermine.objectstore.intermine.DatabaseSchema
Returns an instance of DatabaseSchema, for the given Model and and List of truncated classes.
DatabaseSchema.Fields - Class in org.intermine.objectstore.intermine
Inner class to hold information on Attributes and References.
DatabaseUtil - Class in org.intermine.sql
Collection of commonly used Database utilities
DatabaseUtil.Type - Enum in org.intermine.sql
 
DatabaseWriter - Class in org.intermine.sql.logging
Writes tab-separated Strings to a database table
DatabaseWriter() - Constructor for class org.intermine.sql.logging.DatabaseWriter
Construct an empty DatabaseWriter for testing purposes
DatabaseWriter(Connection, String) - Constructor for class org.intermine.sql.logging.DatabaseWriter
Construct a DatabaseWriter
DataChangedException - Exception in org.intermine.objectstore
An Exception that may be thrown by an ObjectStore indicating that a request cannot be serviced because the database has changed since the request was started.
DataChangedException() - Constructor for exception org.intermine.objectstore.DataChangedException
Constructs an DataChangedException
DataChangedException(String) - Constructor for exception org.intermine.objectstore.DataChangedException
Constructs an DataChangedException with the specified detail message.
DataChangedException(Throwable) - Constructor for exception org.intermine.objectstore.DataChangedException
Constructs an DataChangedException with the specified nested throwable.
DataChangedException(String, Throwable) - Constructor for exception org.intermine.objectstore.DataChangedException
Constructs an DataChangedException with the specified detail message and nested throwable.
DataConverter - Class in org.intermine.dataconversion
Abstract parent class of all DataConverters
DataConverter(ItemWriter, Model) - Constructor for class org.intermine.dataconversion.DataConverter
Constructor that should be called by children
DataConverterStoreHook - Interface in org.intermine.dataconversion
A hook that is called immediately before each Item is stored by the DataConverter.
dataDir - Variable in class org.intermine.task.DirectoryConverterTask
 
DataLoader - Class in org.intermine.dataloader
Loads information from a data source into the InterMine database.
DataLoader(IntegrationWriter) - Constructor for class org.intermine.dataloader.DataLoader
Construct a DataLoader
DataLoaderHelper - Class in org.intermine.dataloader
Class providing utility methods to help with primary key and data source priority configuration
DataService - Class in org.intermine.webservice.server.data
 
DataService(InterMineAPI) - Constructor for class org.intermine.webservice.server.data.DataService
 
DataSetLdr - Interface in org.intermine.web.logic.widget
An Interface which defines a frame in which data can be retrieved, organised and created to then be passed to a JFreeChart for representation
datasource - Variable in class org.intermine.sql.Database
 
dataTracker - Variable in class org.intermine.dataloader.BatchingFetcher
 
DataTracker - Class in org.intermine.dataloader
Interface providing access to data tracking.
DataTracker(Database, int, int) - Constructor for class org.intermine.dataloader.DataTracker
Constructor for DataTracker.
dataTracker - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
 
DATE_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint
 
db - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
DBConverter - Class in org.intermine.dataconversion
A DataConverter that reads from a Database and writes to a ItemWriter
DBConverter(Database, Model, ItemWriter) - Constructor for class org.intermine.dataconversion.DBConverter
Constructor
DBConverterTask - Class in org.intermine.task
Task to call DBConverters.
DBConverterTask() - Constructor for class org.intermine.task.DBConverterTask
 
dbIdsStored - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
dbLog(long, long, long, long, long, Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Produce an entry in the DB log.
dbLog(long, long, long, long, long, Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Produce an entry in the DB log.
decapitalise(String) - Static method in class org.intermine.metadata.StringUtil
Returns a decapitalised version of the given String unless string is an acronym.
declarePrinted() - Method in class org.intermine.webservice.server.output.JSONFormatter
Signal that we have started printing results and that it isn't safe to print headers.
decode(String) - Method in class org.intermine.web.security.Base64PublicKeyDecoder
 
decode(String) - Method in interface org.intermine.web.security.KeyDecoder
Decode the string and make the key.
decodeDbDescription(ObjectStore, String) - Static method in class org.intermine.objectstore.query.ClobAccess
Decodes a String from the database representing a clob object.
decodeLZWString(String) - Static method in class org.intermine.webservice.server.query.QueryRequestParser
Take in a LZW encoded string and return a decoded plain-text string.
DecodingException - Exception in org.intermine.web.security
The error that indicates we cannot decode something.
DecodingException(Throwable) - Constructor for exception org.intermine.web.security.DecodingException
Constructor.
decomposeClass(Class<?>) - Static method in class org.intermine.metadata.Util
Convert a dynamic Class into a Set of Class objects that comprise it.
decomposePath() - Method in class org.intermine.pathquery.Path
Returns a list of paths, each corresponding to one step further along the path.
decompressLZW(List<Integer>) - Static method in class org.intermine.webservice.server.query.QueryRequestParser
Decompress a list of output ks to a string.
DEFAULT - Static variable in class org.intermine.sql.precompute.QueryOptimiserContext
The default context - normal operation with no time limit.
DEFAULT - Static variable in class org.intermine.webservice.client.results.Page
The default page size (from the beginning to the maximum page size)
DEFAULT_ALGORITHM - Static variable in class org.intermine.web.security.KeySigner
The default algorithm to use
DEFAULT_BATCH_SIZE - Static variable in class org.intermine.api.query.PathQueryExecutor
default batch size
DEFAULT_BATCH_SIZE - Static variable in class org.intermine.objectstore.query.ResultsBatches
This is the default batch size for Results objects
DEFAULT_CALLBACK - Static variable in class org.intermine.webservice.server.WebService
Default jsonp callback
DEFAULT_LIMIT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
10 000 000 default size actually means that web service will return all results
DEFAULT_MAX_VALUES - Static variable in class org.intermine.objectstore.ObjectStoreSummary
The default number of values to make available for UI dropdowns - attributes with more values will not become dropdowns.
DEFAULT_MESSAGE - Static variable in class org.intermine.api.bag.BagQueryHelper
Message associated with default bag query.
DEFAULT_OPERATOR - Static variable in class org.intermine.web.logic.Constants
Session attribut containing the default operator name, either 'and' or 'or'.
DEFAULT_REGION_INIT_BATCH_SIZE - Static variable in class org.intermine.bio.web.logic.GenomicRegionSearchService
Default batch size to be used for region search initialisation queries.
DEFAULT_RESULT_SIZE - Static variable in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Default value of size parameter
DEFAULT_TABLE_SIZE - Static variable in class org.intermine.web.logic.Constants
Default size of table implemented by PagedTable.
defaultClsCol - Variable in class org.intermine.bio.dataconversion.IdResolverFactory
 
defaultName - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord
 
defaultNS - Variable in class org.intermine.bio.ontology.OboParser
Default namespace.
DefaultOAuthProvider - Class in org.intermine.web.struts.oauth2
A representation of an OAuth provider which is one of the default providers provided for end-users.
DefaultOAuthProvider(Properties, OAuthProviderType) - Constructor for class org.intermine.web.struts.oauth2.DefaultOAuthProvider
Construct a new provider.
defaultSymbol - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord
 
DelegatedIdentity - Class in org.intermine.web.struts.oauth2
A simple struct class for containing information about a delegated identity.
DelegatedIdentity(String, String, String, String) - Constructor for class org.intermine.web.struts.oauth2.DelegatedIdentity
Construct a new delegated identity.
delete() - Method in class org.intermine.api.bag.SharingInvite
 
delete() - Method in class org.intermine.api.profile.InterMineBag
Delete this bag from the userprofile database, bag should not be used after this method has been called.
delete() - Method in class org.intermine.api.profile.InvalidBag
Delete this bag from the userprofile database, bag should not be used after this method has been called.
DELETE - Static variable in class org.intermine.api.profile.ModelUpdate
label in modelUpdate.properties file to identify deleted classes or fields
delete() - Method in class org.intermine.api.profile.StorableBag
Delete this bag.
delete(InterMineObject) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Delete an object from this ObjectStore, delegate to internal ObjectStoreWriter.
delete(QueryClass, Constraint) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Deletes a set of objects from this ObjectStore.
delete(InterMineObject) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Delete an object from this ObjectStore
delete(QueryClass, Constraint) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Deletes a set of objects from this ObjectStore.
delete(InterMineObject) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Delete an object from this ObjectStore
delete(QueryClass, Constraint) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Deletes a set of objects from this ObjectStore.
delete(PrecomputedTable) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Delete a precomputed table from the underlying database.
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryAction
Delete some queries
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyTemplateAction
Delete some templates.
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.UserTemplateAction
Delete a template query.
delete() - Method in class org.intermine.webservice.client.lists.ItemList
Call for this list to be deleted on the server.
deleteAllBagValues() - Method in class org.intermine.api.profile.InterMineBag
 
deleteAllBagValues() - Method in class org.intermine.api.profile.StorableBag
Remove all the values from the bag-value table.
deleteAllPreferences(Profile) - Method in class org.intermine.api.profile.PreferencesManager
 
deleteApiKey(String) - Method in class org.intermine.dwr.AjaxServices
Delete a user's API key, thus disabling webservice access.
deleteBag(String) - Method in class org.intermine.api.profile.Profile
Delete a bag from the user account, if user is logged in also deletes from the userprofile database.
deleteBags() - Method in class org.intermine.api.profile.ModelUpdate
Delete all bags having as a type one of the classes deleted
deleteBagValues(List<String>) - Method in class org.intermine.api.profile.InterMineBag
Delete a given set of bag values from the bag value table.
deleteBatches - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
deleteFrom(FromElement) - Method in class org.intermine.objectstore.query.Query
Remove a FromElement from the FROM clause
deleteFromGroupBy(QueryNode) - Method in class org.intermine.objectstore.query.Query
Remove a QueryNode from the GROUP BY clause
deleteFromOrderBy(QueryOrderable) - Method in class org.intermine.objectstore.query.Query
Remove a QueryOrderable from the ORDER BY clause
deleteFromSelect(QuerySelectable) - Method in class org.intermine.objectstore.query.Query
Remove a QuerySelectable from the SELECT clause
deleteGlobalRepository(Profile) - Method in class org.intermine.api.search.GlobalRepository
 
deleteHistory(String) - Method in class org.intermine.api.profile.Profile
Remove an item from the query history.
deleteIndexDirectory() - Static method in class org.intermine.api.lucene.KeywordSearch
delete the directory used for the index (used in postprocessing)
deleteLargeBinary(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager
Delete a large object from the database based on a given metadata key.
deleteList(ItemList) - Method in class org.intermine.webservice.client.services.ListService
Deletes a list on the server.
deleteObjectTags(String, String, String) - Method in class org.intermine.api.profile.TagManager
Deletes all tags assigned to a specified object.
deletePreference(Profile, String) - Method in class org.intermine.api.profile.PreferencesManager
 
DeletePreferencesService - Class in org.intermine.webservice.server.user
A service that deletes a user's preferences.
DeletePreferencesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.DeletePreferencesService
 
deleteProfile(Profile) - Method in class org.intermine.api.profile.ProfileManager
Completely remove a profile and all of its associated data from the data-store.
deleteQuery(String) - Method in class org.intermine.api.profile.Profile
Delete a query
deleteRow(Connection, String, String, Object) - Method in class org.intermine.sql.writebatch.Batch
Deletes a row from the batch for a given table.
deleteRow(Connection, String, String, String, int, int) - Method in class org.intermine.sql.writebatch.Batch
Deletes a row from the batch for a given indirection table.
deleteRow(int, int) - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Deletes a row from the batch.
deleteRow(String, Object) - Method in class org.intermine.sql.writebatch.TableBatch
Deletes a row from the batch.
deleteSomeBagValues(List<String>) - Method in class org.intermine.api.profile.StorableBag
Delete a given set of bag values from the bag value table.
deleteTableFromDatabase(String) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Delete a PrecomputedTable from the database.
deleteTag(Tag) - Method in class org.intermine.api.profile.TagManager
Delete a tag object from the database.
deleteTag(String, WebSearchable, Profile) - Method in class org.intermine.api.profile.TagManager
Delete a tag by name from a web-searchable object.
deleteTag(String, ClassDescriptor, Profile) - Method in class org.intermine.api.profile.TagManager
Delete a tag by name from a class-descriptor.
deleteTag(String, ReferenceDescriptor, Profile) - Method in class org.intermine.api.profile.TagManager
Delete a tag by name from a reference-descriptor.
deleteTag(String, String, String, String) - Method in class org.intermine.api.profile.TagManager
Deletes a tag object from the database.
deleteTag(String, String, String) - Static method in class org.intermine.dwr.AjaxServices
Deletes tag.
deleteTags(String, String, String, String) - Method in class org.intermine.api.profile.TagManager
Deletes tags object from the database.
deleteTemplate(String, TrackerDelegate, boolean) - Method in class org.intermine.api.profile.Profile
Delete a template and its tags, rename the template tracks adding the prefix "deleted_" to the previous name.
deleteTempTableSize - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
DeleteTokensService - Class in org.intermine.webservice.server.user
Service which ensures that the authenticating user has no tokens.
DeleteTokensService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.DeleteTokensService
 
deleteUserToShareBag(String, String) - Method in class org.intermine.dwr.AjaxServices
Un-share the bag given in input with the user which userName is input
deleteWithConnection(Connection, InterMineObject) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Performs a delete, with a connection.
deleteWithConnection(Connection, QueryClass, Constraint) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Performs a delete, with a connection.
DeletionEvent - Class in org.intermine.api.search
A representation of a notification that a websearchable has been deleted.
DeletionEvent(WebSearchable) - Constructor for class org.intermine.api.search.DeletionEvent
Constructor.
DeletionToken - Class in org.intermine.webservice.server.user
A class representing a deletion token.
DeletionToken(Profile, UUID, Date) - Constructor for class org.intermine.webservice.server.user.DeletionToken
 
DeletionTokenCancellationService - Class in org.intermine.webservice.server.user
A service that cancels the profile deletion process by deleting the token that could be used to complete it.
DeletionTokenCancellationService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.user.DeletionTokenCancellationService
 
DeletionTokenInfoService - Class in org.intermine.webservice.server.user
A service that retrieves information about a deletion token.
DeletionTokenInfoService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.user.DeletionTokenInfoService
 
DeletionTokens - Class in org.intermine.webservice.server.user
A class that manages deletion tokens for the lifespan of a webapp.
DELIM - Static variable in class org.intermine.objectstore.intermine.NotXmlParser
The string that delimits the sections of the NotXml.
DelimitedFileConfiguration - Class in org.intermine.task
This class specifies how the values in a tab or comma separated file should be used to fill in objects in an ObjectStore.
DelimitedFileConfiguration(Model, InputStream) - Constructor for class org.intermine.task.DelimitedFileConfiguration
Create a new DelimitedFileConfiguration from an InputStream.
densities(Command) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
densities(Command) - Method in class org.intermine.webservice.server.jbrowse.genomic.Engine
 
Dependencies - Class in org.intermine.task
Find and compile/execute dependent project (via the project.properties files)
Dependencies() - Constructor for class org.intermine.task.Dependencies
 
deregisterRequestId(Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
This method deregisters a Thread from a request ID.
deregisterStatement(Statement) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
This method deregisters a Statement for the request ID of the current thread.
DeregistrationService - Class in org.intermine.webservice.server.user
 
DeregistrationService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.DeregistrationService
 
DeregistrationTokenServlet - Class in org.intermine.webservice.server.user
A servlet for routing requests to do with deregistration.
DeregistrationTokenServlet() - Constructor for class org.intermine.webservice.server.user.DeregistrationTokenServlet
 
description - Variable in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder
 
description - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
DESCRIPTION_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
The description
DescriptorUtils - Class in org.intermine.metadata
 
deSelectId(String, String) - Static method in class org.intermine.dwr.AjaxServices
remove an Id from the PagedTable
deSelectId(Integer) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Remove the object with the given object id from the list of selected objects.
destDir - Variable in class org.intermine.task.ModelOutputTask
 
destDir - Variable in class org.intermine.task.RetrieveMetadataTask
 
destFile - Variable in class org.intermine.objectstore.intermine.TorqueModelOutputTask
 
destroy() - Method in class org.intermine.web.filters.ExpiresHeaderFilter
destroy() - Method in class org.intermine.web.filters.HeaderFilter
destroy() - Method in class org.intermine.web.filters.ReleaseEtagFilter
 
destroy() - Method in class org.intermine.web.filters.SetCharacterEncodingFilter
Take this filter out of service.
destroy() - Method in class org.intermine.web.struts.InitialiserPlugin
Destroy method called at Servlet destroy.
destroy() - Method in class org.intermine.webservice.server.filter.RequestSubClassFilter
 
destroy() - Method in class org.intermine.webservice.server.idresolution.IdResolutionServlet
 
determineType(String) - Method in class org.intermine.bio.dataconversion.EnsemblSnpDbConverter
Given an allele string read from the database determine the type of variation, e.g. snp, in-del, etc.
deVerify() - Method in class org.intermine.pathquery.PathQuery
 
DevNullMap<K,V> - Class in org.intermine.api.util
An implementation of Map that is totally forgetful.
DevNullMap() - Constructor for class org.intermine.api.util.DevNullMap
 
didNotExplain(BestQueryExplainer.Candidate) - Method in class org.intermine.sql.precompute.BestQueryExplainer
Internal method that records that a query was not explained.
didNotExplain(BestQueryExplainer.Candidate) - Method in class org.intermine.sql.precompute.BestQueryExplainerVerbose
Internal method that records that a query was not explained.
diff(ItemList...) - Method in class org.intermine.webservice.client.services.ListService
Find the symmetric difference of one or more lists to produce a new list.
diff(ListService.ListOperationInfo, ItemList...) - Method in class org.intermine.webservice.client.services.ListService
Find the symmetric difference of one or more lists to produce a new list.
diff(Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService
Find the symmetric difference of one or more lists to produce a new list.
diff(ListService.ListOperationInfo, Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService
Find the symmetric difference of one or more lists to produce a new list.
DirectDataLoader - Class in org.intermine.dataloader
A DataLoader with helper methods for creating and storing objects using an IntegrationWriter.
DirectDataLoader(IntegrationWriter, String, String) - Constructor for class org.intermine.dataloader.DirectDataLoader
Create a new DirectDataLoader using the given IntegrationWriter and source name.
DirectDataLoaderTask - Class in org.intermine.task
This task uses a DirectDataLoader to create objects and store them directly into an ObjectStore using an IntegrationWriter.
DirectDataLoaderTask() - Constructor for class org.intermine.task.DirectDataLoaderTask
 
directory - Variable in class org.intermine.task.InheritanceDotTask
 
DirectoryConverter - Class in org.intermine.dataconversion
Parent class for DataConverters that read from directories
DirectoryConverter(ItemWriter, Model) - Constructor for class org.intermine.dataconversion.DirectoryConverter
Constructor
DirectoryConverterTask - Class in org.intermine.task
Initiates retrieval and conversion of data from a source directory.
DirectoryConverterTask() - Constructor for class org.intermine.task.DirectoryConverterTask
 
disableResultsCache - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
disableSaving() - Method in class org.intermine.api.profile.Profile
Disable saving until enableSaving() is called.
DisclosureBodyTag - Class in org.intermine.web.tags.disclosure
This class renders disclosureBody tag.
DisclosureBodyTag() - Constructor for class org.intermine.web.tags.disclosure.DisclosureBodyTag
 
DisclosureDetailsTag - Class in org.intermine.web.tags.disclosure
This class renders disclosureDetails tag.
DisclosureDetailsTag() - Constructor for class org.intermine.web.tags.disclosure.DisclosureDetailsTag
 
DisclosureHeadTag - Class in org.intermine.web.tags.disclosure
This class renders disclosureHead tag.
DisclosureHeadTag() - Constructor for class org.intermine.web.tags.disclosure.DisclosureHeadTag
 
DisclosureTag - Class in org.intermine.web.tags.disclosure
This class renders disclosure tag.
DisclosureTag() - Constructor for class org.intermine.web.tags.disclosure.DisclosureTag
 
DisclosureTitleTag - Class in org.intermine.web.tags.disclosure
This class renders disclosureTitle tag.
DisclosureTitleTag() - Constructor for class org.intermine.web.tags.disclosure.DisclosureTitleTag
 
DiseaseDisplayer - Class in org.intermine.bio.web.displayer
For ratmine, display all disease ontology objects for orthologues
DiseaseDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.DiseaseDisplayer
Construct with config and the InterMineAPI.
display(HttpServletRequest, ReportObject) - Method in class org.flymine.web.displayer.DrosophilaHomologueDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.flymine.web.displayer.FlyAtlasDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.flymine.web.displayer.RNAiDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.ComplexDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.CuratedProteinsDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.CytoscapeNetworkDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.DiseaseDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.EsynDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.FlyBaseExpressionDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.GBrowseDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.GeneExpressionAtlasDiseasesDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.GeneExpressionAtlasTissuesDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.GeneIdentifiersDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.GeneOntologyDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.GeneStructureDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.HomologueDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.JBrowseDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.JMOLDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.MinePathwaysDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.MouseAllelesDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.OverlappingFeaturesDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.PathwayDescriptionDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.PathwaysDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.ProteinAtlasDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.ProteinSequenceDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.ProteinStructureATMDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.PublicationAnnotationsDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.PublicationCountsDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.RegulatoryRegionsDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.ReportWidgetDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.SequenceFeatureDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.SnpToGeneDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.UniProtCommentsDisplayer
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.web.displayer.ReportDisplayer
To be implemented in subclasses where any specific information to be displayed should be put on the request.
DisplayCollection - Class in org.intermine.web.logic.results
Class to represent a collection field of an object for the webapp
DisplayCollection(Collection<?>, CollectionDescriptor, WebConfig, Properties, Map<String, List<FieldDescriptor>>, List<Class<?>>) - Constructor for class org.intermine.web.logic.results.DisplayCollection
Construct a new DisplayCollection object
DisplayCollection(Collection<?>, CollectionDescriptor, WebConfig, Properties, Map<String, List<FieldDescriptor>>, List<Class<?>>, String) - Constructor for class org.intermine.web.logic.results.DisplayCollection
Construct a DisplayCollection object.
DisplayConstraint - Class in org.intermine.web.logic.query
Representation of a PathQuery constraint for use by JSP pages.
DisplayConstraint(Path, Profile, PathQuery, AutoCompleter, ObjectStoreSummary, BagQueryConfig, Map<String, List<FieldDescriptor>>, BagManager) - Constructor for class org.intermine.web.logic.query.DisplayConstraint
Construct for a new constraint that is being added to a query.
DisplayConstraint.DisplayConstraintOption - Class in org.intermine.web.logic.query
Representation of a constraint operation to populate a dropdown.
DisplayConstraint.DisplayConstraintOption(String, Integer) - Constructor for class org.intermine.web.logic.query.DisplayConstraint.DisplayConstraintOption
Construct with the constraint lable and index
DisplayConstraintFactory - Class in org.intermine.web.logic.query
A class that will help you manufacture instances of DisplayConstraint.
DisplayConstraintFactory(InterMineAPI, AutoCompleter) - Constructor for class org.intermine.web.logic.query.DisplayConstraintFactory
Get an object that creates display constraints.
DisplayConstraintHelpMessages - Class in org.intermine.web.logic.query
Class to generate help messages appropriate to a given constraint for display in the QueryBuilder and template form.
Displayer - Class in org.intermine.web.logic.config
Configuration object describing details of a displayer
Displayer() - Constructor for class org.intermine.web.logic.config.Displayer
 
DisplayerManager - Class in org.intermine.web.displayer
Read in and provide access to report page displayers.
DisplayField - Class in org.intermine.web.logic.results
Class to represent a field of an object for the webapp
DisplayField(Collection<?>, FieldDescriptor, WebConfig, Properties, Map<String, List<FieldDescriptor>>, List<Class<?>>) - Constructor for class org.intermine.web.logic.results.DisplayField
Create a new DisplayField object.
DisplayField(Collection<?>, FieldDescriptor, WebConfig, Properties, Map<String, List<FieldDescriptor>>, List<Class<?>>, String) - Constructor for class org.intermine.web.logic.results.DisplayField
Create a new DisplayField object.
DisplayLookupMessageHandler - Class in org.intermine.web.struts
 
DisplayLookupMessageHandler() - Constructor for class org.intermine.web.struts.DisplayLookupMessageHandler
 
DisplayPath - Class in org.intermine.web.logic.querybuilder
A small wrapper around Path with more jsp-accessible data.
DisplayPath(Path) - Constructor for class org.intermine.web.logic.querybuilder.DisplayPath
Constructs a new DisplayPath object from a Path.
DisplayReference - Class in org.intermine.web.logic.results
Class to represent a reference field of an object for display in the webapp
DisplayReference(ProxyReference, ReferenceDescriptor, WebConfig, Map<String, List<FieldDescriptor>>, String) - Constructor for class org.intermine.web.logic.results.DisplayReference
Create a new DisplayReference object.
distinct - Variable in class org.intermine.sql.query.Query
 
DIVIDE - Static variable in class org.intermine.objectstore.query.QueryExpression
Division of two numeric fields
DIVIDE - Static variable in class org.intermine.sql.query.Function
DIVIDE function - takes two operands.
DO_NOTHING_ACTION - Static variable in class org.intermine.bio.dataconversion.SequenceProcessor
An action that does nothing - used to ignore a synonym/dbxref/whatever instead of doing the default.
DO_SOURCES - Static variable in class org.intermine.task.PostProcessTask
Used mainly in project.xml indicate when we should iterate over the source directories when we are doing the postprocessing, as some postprocess tasks will have to run before the source tasks and some other tasks afterwards.
doAdditionalConstraintStuff(PathQuery, PathConstraint, XMLStreamWriter) - Method in class org.intermine.pathquery.PathQueryBinding
Adds any extra information for a constraint, like say Template extras.
doAdditionalConstraintStuff(PathQuery, PathConstraint, XMLStreamWriter) - Method in class org.intermine.template.xml.TemplateQueryBinding
Adds any extra information for a constraint, like say Template extras.
doAnalyse(String, Connection) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Performs an ANALYSE of a table.
doDelete(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.core.WebServiceServlet
 
doDeletes(String, TableBatch) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Performs all the deletes for the given table name and table batch.
DOES_NOT_CONTAIN - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument does not contain the second
DOES_NOT_EXIST - Static variable in class org.intermine.metadata.ConstraintOp
Subquery does not exist
DOES_NOT_HAVE - Static variable in class org.intermine.metadata.ConstraintOp
Require that the left argument does not have any of the right argument.
DOES_NOT_MATCH - Static variable in class org.intermine.metadata.ConstraintOp
Require that the two arguments do not match
DOES_NOT_OVERLAP - Static variable in class org.intermine.metadata.ConstraintOp
Require that a range does not overlap another range
doesNotContain(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to not contain a value.
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.web.filters.ExpiresHeaderFilter
Add an expires header to matching files to help browsers avoid reloading static files.
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.web.filters.HeaderFilter
Do the filtering.
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.web.filters.ReleaseEtagFilter
 
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.web.filters.SetCharacterEncodingFilter
Select and set (if specified) the character encoding to be used to interpret request parameters for this request.
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.webservice.server.filter.RequestSubClassFilter
 
doFinalise() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Finalise this object.
doFinalise() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Overrides Object.finalize - release the connection back to the objectstore.
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.logic.login.OpenIDAuthenticator
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.AvailableServicesServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.ClassKeyServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.core.WebServiceServlet
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.model.ModelServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.path.PossibleValuesServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.CodeServlet
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryListAppendServlet
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryToListServlet
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.result.QueryResultServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.SchemaServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.ServicesListingsServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.SummaryServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.template.TemplateListAppendServlet
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.user.TokenServlet
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.VersionServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.AvailableWidgetsServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.GraphWidgetsServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.TableWidgetsServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.WidgetsServlet
}
doIndirectionDeletes(String, IndirectionTableBatch) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Performs all the delete operations for the given IndirectionTableBatch and name.
doIndirectionInserts(String, IndirectionTableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
Performs all the insert operations for the given IndirectionTableBatch and name.
doIndirectionInserts(String, IndirectionTableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl
Performs all the insert operations for the given IndirectionTableBatch and name.
doIndirectionInserts(String, IndirectionTableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Performs all the insert operations for the given IndirectionTableBatch and name.
doInserts(String, TableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
Performs all the inserts for the given table name and table batch.
doInserts(String, TableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl
Performs all the inserts for the given table name and table batch.
doInserts(String, TableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Performs all the inserts for the given table name and table batch.
doLiftOver(GenomicRegionSearchConstraint, String, String, String, String) - Method in class org.intermine.bio.web.logic.LiftOverService
Send a HTTP POST request to liftOver service.
doListCreation(GenomicRegionSearchListInput, Profile, String) - Method in class org.intermine.bio.webservice.GenomicRegionSearchService
Create the list specified by the region search input.
doLogin(HttpServletRequest, String, String) - Method in class org.intermine.web.logic.profile.LoginHandler
Log-in a user.
doMarshal(PathQuery, String, String, XMLStreamWriter, int) - Method in class org.intermine.pathquery.PathQueryBinding
Marshal to an XMLStreamWriter.
doMarshal(TemplateQuery, XMLStreamWriter, int) - Method in class org.intermine.template.xml.TemplateQueryBinding
Convert a TemplateQuery to XML and write XML to given writer.
DoNothingAction - Class in org.intermine.bio.chado.config
An action that does nothing.
DoNothingAction() - Constructor for class org.intermine.bio.chado.config.DoNothingAction
 
DoNothingIdResolver - Class in org.intermine.bio.dataconversion
An IdResolver for use in tests that will always resolve an id to the input id given.
DoNothingIdResolver(String) - Constructor for class org.intermine.bio.dataconversion.DoNothingIdResolver
Construct and empty IdResolver
DoNothingIdResolverFactory - Class in org.intermine.bio.dataconversion
Construct a DoNothingIdResolver that will resolve every id to the id that was given as input.
DoNothingIdResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.DoNothingIdResolverFactory
Construct with class name for mock IdResolver
doPk(PrimaryKey, ClassDescriptor, Map<InterMineObject, Set<InterMineObject>>, List<InterMineObject>, Set<Integer>) - Method in class org.intermine.dataloader.BatchingFetcher
Fetches equivalent objects for a particular primary key.
doPks(Map<PrimaryKey, ClassDescriptor>, Map<InterMineObject, Set<InterMineObject>>, Map<ClassDescriptor, List<InterMineObject>>, long) - Method in class org.intermine.dataloader.BatchingFetcher
Fetches data for the given primary keys.
doPks(Map<PrimaryKey, ClassDescriptor>, Map<InterMineObject, Set<InterMineObject>>, Map<ClassDescriptor, List<InterMineObject>>, long) - Method in class org.intermine.dataloader.ParallelBatchingFetcher
Fetches data for the given primary keys.
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.AvailableServicesServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.core.WebServiceServlet
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.model.ModelServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.path.PossibleValuesServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.CodeServlet
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryListAppendServlet
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryToListServlet
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.result.QueryResultServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.ServicesListingsServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.template.TemplateListAppendServlet
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.VersionServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.GraphWidgetsServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.TableWidgetsServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.WidgetsServlet
}
doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.AvailableServicesServlet
}
doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.core.WebServiceServlet
 
doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryListAppendServlet
doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryToListServlet
doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.template.TemplateListAppendServlet
doQueryGetPagedTable(HttpServletRequest, InterMineBag) - Static method in class org.intermine.web.logic.session.SessionMethods
Execute a query and return a PagedTable to display contents of an InterMineBag
doQueryGetPagedTable(HttpServletRequest, InterMineObject, String, String) - Static method in class org.intermine.web.logic.session.SessionMethods
Execute a query and return a PagedTable to display contents of a Collection, field of a given InterMineObject.
doReplace() - Method in class org.intermine.webservice.server.lists.ListInput
 
doRequest(ResultsBatches, int, boolean, boolean) - Static method in class org.intermine.objectstore.query.PrefetchManager
Returns when the given request is completed.
doRequest(PrefetchManager.Request) - Static method in class org.intermine.objectstore.query.PrefetchManager
Returns the batch described by the request.
doShutdown() - Static method in class org.intermine.web.context.InterMineContext
Send the signal that shutdown is happening - try and release resources.
doSQL(ObjectStore) - Method in class org.intermine.task.ConverterTask
Runs various performance-enhancing SQL statements.
doStaticLogin(HttpServletRequest, String, String) - Static method in class org.intermine.web.logic.profile.LoginHandler
Main log-in logic.
doSummarise - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
doTag() - Method in class org.intermine.web.tags.disclosure.DisclosureBodyTag
Renders tag.
doTag() - Method in class org.intermine.web.tags.disclosure.DisclosureDetailsTag
Renders tag.
doTag() - Method in class org.intermine.web.tags.disclosure.DisclosureHeadTag
Renders tag.
doTag() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Renders tag.
doTag() - Method in class org.intermine.web.tags.disclosure.DisclosureTitleTag
Renders tag.
doTag() - Method in class org.intermine.web.tags.table.NavigationBarTag
According pageSize and currentPage parameter navigation bar computes link to following and previous page.
doTag() - Method in class org.intermine.web.tags.table.TableTag
doTag() - Method in class org.intermine.web.tags.util.TreatStringTag
 
doTrackerFor(Class<?>) - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Returns true if the given class is NOT a subclass of any of the classes in trackerMissingClasses.
doUpgrade() - Method in interface org.intermine.api.bag.IdUpgrader
Return true if upgrade should be performed
doUpgrade() - Method in class org.intermine.web.bag.PkQueryIdUpgrader
Return true if upgrade should be performed.
download(String) - Method in class org.intermine.web.util.HttpClient
 
doWrite() - Method in class org.intermine.dataloader.DataTracker
Performs maintenance of the cache, writing stuff to the backing database.
drainToPrintStream(PrintStream) - Method in class org.intermine.bio.util.ClobAccessReverseComplement
Sends the entire contents of the Clob into the given PrintStream.
drainToPrintStream(PrintStream) - Method in class org.intermine.objectstore.query.ClobAccess
Sends the entire contents of the Clob into the given PrintStream.
driver - Variable in class org.intermine.sql.Database
 
dropAffected(Set<String>) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Deletes all precomputed tables that would be affected by changes in any table in a given list of table names.
dropEverything() - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Deletes every single precomputed table.
dropIndex(WebSearchable) - Method in class org.intermine.api.search.SearchRepository
Drop the index that contains information about the websearchable object passed in.
dropIndex(String, int) - Method in class org.intermine.task.CreateIndexesTask
Drop an index by name, ignoring any resulting errors
DropPrecomputedTablesTask - Class in org.intermine.task
A Task that drops all precomputed tables in an ObjectStore.
DropPrecomputedTablesTask() - Constructor for class org.intermine.task.DropPrecomputedTablesTask
 
DrosophilaHomologueDisplayer - Class in org.flymine.web.displayer
Displayer for drosophila homologue data
DrosophilaHomologueDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.flymine.web.displayer.DrosophilaHomologueDisplayer
 
DummyExplainResult - Class in org.intermine.sql.query
Subclass of ExplainResult not associated with a database.
DummyExplainResult(Query) - Constructor for class org.intermine.sql.query.DummyExplainResult
Constructs an instance of PostgresExplainResult without any data.
DumpDefaultTemplatesTask - Class in org.intermine.web.task
Dump templates and configuration tags.
DumpDefaultTemplatesTask() - Constructor for class org.intermine.web.task.DumpDefaultTemplatesTask
 
DUPLICATE - Static variable in class org.intermine.api.bag.BagQueryResult
Key of the Map returned by getIssues() when the query for the input string found more than one object.
DuplicateMappingException - Exception in org.intermine.api.profile
 
DuplicateMappingException(String, String) - Constructor for exception org.intermine.api.profile.DuplicateMappingException
 
duplicateObjects - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
This is a list of the objects in the destination database that we have written to as a non-skeleton more than once.
duplicateQuotes(String) - Static method in class org.intermine.metadata.StringUtil
Duplicates single quotes in Strings for correct storage in postgres.
DynamicAttributeTask - Class in org.intermine.task
An ant task that provides a method for setting attributes dynamically within a class.
DynamicAttributeTask() - Constructor for class org.intermine.task.DynamicAttributeTask
 
DynamicBean - Class in org.intermine.util
Class which represents a generic bean
DynamicBean() - Constructor for class org.intermine.util.DynamicBean
Construct the interceptor
DynamicUtil - Class in org.intermine.util
Utilities to create DynamicBeans

E

earlyExtraProcessing(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Do any extra processing that is needed before the converter starts querying features
earlyExtraProcessing(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Do any extra processing that is needed before the converter starts querying features
earlyItems - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler
 
editable - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
editableConstraints - Variable in class org.intermine.template.TemplateQuery
List of those Constraints that are editable
editConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Edit a constraint on the query identified by the constraint code.
edited - Variable in class org.intermine.template.TemplateQuery
Whether this is an edited version of another template.
EDITING_TEMPLATE - Static variable in class org.intermine.web.logic.Constants
Session attribute used to store the status editing template
editJoinStyle(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Edit a the join style settings for a path.
EditPropertiesAction - Class in org.intermine.web.struts
A controller to edit the properties of a running application.
EditPropertiesAction() - Constructor for class org.intermine.web.struts.EditPropertiesAction
 
EditPropertiesForm - Class in org.intermine.web.struts
An overly verbose way of passing parameters back to the controller.
EditPropertiesForm() - Constructor for class org.intermine.web.struts.EditPropertiesForm
 
EditTemplateAction - Class in org.intermine.web.struts
Action to edit a user template query.
EditTemplateAction() - Constructor for class org.intermine.web.struts.EditTemplateAction
 
editTemplateConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Edit a constraint's template settings identified by code in query.
EFETCH_URL - Static variable in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
 
Either<A,B> - Class in org.intermine.webservice.server.core
Disjoint type union Disjoint type union to handle certain features of the way we present results in outer-joined tables, but abstracted to be made more generally useful, and incorportating the visitor pattern for value access.
Either.Left<A,B> - Class in org.intermine.webservice.server.core
 
Either.Left(A) - Constructor for class org.intermine.webservice.server.core.Either.Left
Construct a left.
Either.Right<A,B> - Class in org.intermine.webservice.server.core
 
Either.Right(B) - Constructor for class org.intermine.webservice.server.core.Either.Right
Construct a right.
EitherVisitor<A,B,T> - Class in org.intermine.webservice.server.core
A mapping function capable of accessing a disjoint sum-type (an Either A B).
EitherVisitor() - Constructor for class org.intermine.webservice.server.core.EitherVisitor
 
EMAIL - Static variable in class org.intermine.api.profile.UserPreferences
This is known to the API as the Profile needs to read this to provide getEmailAddress().
email(String, String) - Method in class org.intermine.util.Emailer
Send a message to a user.
email(String, String, Object...) - Method in class org.intermine.util.Emailer
Send a message to a user with some data.
email(String, String, String, String, Properties) - Static method in class org.intermine.util.MailUtils
Send an email to an address, supplying the recipient, subject and body.
email(String, String, String, Properties) - Static method in class org.intermine.util.MailUtils
 
email(String, String) - Method in class org.intermine.web.context.NullMailer
 
email(String, String, Object...) - Method in class org.intermine.web.context.NullMailer
 
Emailer - Class in org.intermine.util
A class that will send emails to people.
Emailer(Properties) - Constructor for class org.intermine.util.Emailer
Instantiate an emailer.
EmailerFactory - Class in org.intermine.web.context
 
emailPasswordToken(String, String, Properties) - Static method in class org.intermine.util.MailUtils
Send a password change email to an email address
EmployeeExporter - Class in org.intermine.model.testmodel.web
An implementation of TableExporter that exports Employee objects.
EmployeeExporter() - Constructor for class org.intermine.model.testmodel.web.EmployeeExporter
 
EmploymentPeriodHelper - Class in org.intermine.model.testmodel.query.range
 
EmploymentPeriodHelper() - Constructor for class org.intermine.model.testmodel.query.range.EmploymentPeriodHelper
 
emptyAttributesMap - Variable in class org.intermine.objectstore.ObjectStoreSummary
 
emptyFieldsMap - Variable in class org.intermine.objectstore.ObjectStoreSummary
 
enableSaving() - Method in class org.intermine.api.profile.Profile
Re-enable saving when saveTemplate(), deleteQuery() etc. are called.
enableSaving() - Method in class org.intermine.api.util.AnonProfile
 
EncloseSubqueryBestQuery - Class in org.intermine.sql.precompute
This object is a BestQuery tracker that encloses all added queries into a surrounding query as a subquery, and passes them onto another BestQuery tracker.
EncloseSubqueryBestQuery(BestQuery, String, String) - Constructor for class org.intermine.sql.precompute.EncloseSubqueryBestQuery
Constructor.
encode(Object) - Static method in class org.intermine.webservice.server.LinkGeneratorBase
Encodes object string value to be able to be part of url.
encode(Object) - Static method in class org.intermine.webservice.server.query.result.QueryResultService
URL Encode an object.
ENCODED_DELIM - Static variable in class org.intermine.objectstore.intermine.NotXmlParser
The character that denotes an encoded delimiter in the string.
encodeString(String) - Static method in class org.intermine.web.util.URLUtil
Encodes string to be URL safe.
encodeURL(String) - Static method in class org.intermine.web.util.URLUtil
Encodes URL.
encoding - Variable in class org.intermine.web.filters.SetCharacterEncodingFilter
The default character encoding to set for requests that pass through this filter.
end - Variable in class org.intermine.objectstore.query.OverlapRange
 
endDocument() - Method in class org.intermine.webservice.server.ServiceListingHandler
 
endElement(String, String, String) - Method in class org.intermine.api.bag.BagQueryHandler
endElement(String, String, String) - Method in class org.intermine.api.bag.InvitationHandler
endElement(String, String, String) - Method in class org.intermine.api.profile.PreferencesHandler
endElement(String, String, String) - Method in class org.intermine.api.profile.TagHandler
endElement(String, String, String) - Method in class org.intermine.api.tracker.xml.TrackManagerHandler
endElement(String, String, String) - Method in class org.intermine.api.xml.InterMineBagHandler
endElement(String, String, String) - Method in class org.intermine.api.xml.SavedQueryHandler
endElement(String, String, String) - Method in class org.intermine.api.xml.SharedBagHandler
endElement(String, String, String) - Method in class org.intermine.pathquery.PathQueryHandler
endElement(String, String, String) - Method in class org.intermine.template.xml.TemplateQueryHandler
endElement(String, String, String) - Method in class org.intermine.webservice.server.ServiceListingHandler
 
endElement(String, String, String) - Method in class org.intermine.xml.full.FullHandler
endIsAttribute() - Method in class org.intermine.pathquery.Path
Return true if and only if the end of the path is an attribute.
endIsCollection() - Method in class org.intermine.pathquery.Path
Return true if and only if the end of the path is a collection.
endIsReference() - Method in class org.intermine.pathquery.Path
Return true if and only if the end of the path is a reference .
endl - Variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
ENDL - Static variable in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
 
ENDL - Static variable in class org.intermine.bio.dataconversion.PdbConverter
 
ENDL - Static variable in class org.intermine.codegen.JavaModelOutput
 
ENDL - Static variable in class org.intermine.metadata.ClassDescriptor
 
ENDL - Static variable in class org.intermine.metadata.Model
 
ENDL - Static variable in class org.intermine.objectstore.intermine.TorqueModelOutput
 
ENDL - Static variable in class org.intermine.xml.full.FullRenderer
 
Endpoint - Class in org.intermine.webservice.server.jbrowse
 
Endpoint(InterMineAPI) - Constructor for class org.intermine.webservice.server.jbrowse.Endpoint
 
Engine - Class in org.intermine.webservice.server.jbrowse.genomic
An adaptor for running JBrowse queries against a genomic database.
Engine(InterMineAPI) - Constructor for class org.intermine.webservice.server.jbrowse.genomic.Engine
constructor
EnrichmentCalculation - Class in org.intermine.web.logic.widget
Calculate enrichment of an attribute applied to members of a sample that is a subset of a larger population.
EnrichmentInput - Interface in org.intermine.web.logic.widget
Define methods to access data an enrichment calculation needs to be provided with.
EnrichmentInputWidgetLdr - Class in org.intermine.web.logic.widget
Executes queries and summarises data for a specific EnrichmentWidgetLdr ready for calculation.
EnrichmentInputWidgetLdr(ObjectStore, EnrichmentWidgetImplLdr) - Constructor for class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
Construct with an EnrichmentWidgetLdr that contains queries needed for specific widget tests.
EnrichmentJSONProcessor - Class in org.intermine.webservice.server.widget
 
EnrichmentOptions - Interface in org.intermine.web.logic.widget
The type of options that enrichment widgets expect to receive.
EnrichmentResultProcessor - Interface in org.intermine.webservice.server.widget
The type of objects that can process enrichment results for serialisation to the outside world.
EnrichmentResults - Class in org.intermine.web.logic.widget
A container for results from an Enrichment analysis.
EnrichmentResults(Map<String, BigDecimal>, Map<String, Integer>, Map<String, String>, int) - Constructor for class org.intermine.web.logic.widget.EnrichmentResults
Construct with pre-populated maps from enriched attributes to p-values, counts and labels.
EnrichmentWidget - Class in org.intermine.web.logic.widget
 
EnrichmentWidget(EnrichmentWidgetConfig, InterMineBag, InterMineBag, ObjectStore, EnrichmentOptions) - Constructor for class org.intermine.web.logic.widget.EnrichmentWidget
 
EnrichmentWidgetConfig - Class in org.intermine.web.logic.widget.config
A description of an enrichment calculation.
EnrichmentWidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
EnrichmentWidgetForm - Class in org.intermine.web.struts
 
EnrichmentWidgetForm() - Constructor for class org.intermine.web.struts.EnrichmentWidgetForm
Constructor
EnrichmentWidgetImplLdr - Class in org.intermine.web.logic.widget
Implement methods to access data an enrichment calculation needs to be provided with.
EnrichmentWidgetImplLdr(InterMineBag, InterMineBag, ObjectStore, EnrichmentWidgetConfig, String, boolean, CorrectionCoefficient) - Constructor for class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr
Construct an Enrichment widget loader, which performs the queries needed for enrichment statistics.
EnrichmentWidgetResultService - Class in org.intermine.webservice.server.widget
Web service that returns the result of an enrichment calculation over a list of objects.
EnrichmentWidgetResultService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.EnrichmentWidgetResultService
 
EnrichmentXMLProcessor - Class in org.intermine.webservice.server.widget
A widget result processor for enrichment results that produces output as XML.
EnsemblComparaConverter - Class in org.intermine.bio.dataconversion
Converter that process 4 column text file and produces homologues.
EnsemblComparaConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.EnsemblComparaConverter
Constructor
ensemblDb - Variable in class org.intermine.bio.postprocess.PostProcessOperationsTask
 
EnsemblGwasDbConverter - Class in org.intermine.bio.dataconversion
Load Genome Wide Association Study (GWAS) data from Ensembl variation mySQL database.
EnsemblGwasDbConverter(Database, Model, ItemWriter) - Constructor for class org.intermine.bio.dataconversion.EnsemblGwasDbConverter
Construct a new EnsemblGwasDbConverter.
EnsemblGwasDbPostprocess - Class in org.intermine.bio.postprocess
Update GWAS objects with name and firstAuthor from referenced publication.
EnsemblGwasDbPostprocess(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.EnsemblGwasDbPostprocess
Create a new GWAS post processor from an ObjectStoreWriter
EnsemblIdResolverFactory - Class in org.intermine.bio.dataconversion
Create an IdResolverFactory for human Ensembl gene ids, this doesn't include any synonyms or id tracking but simply filters for ids that are located on a the main chromosomes.
EnsemblIdResolverFactory() - Constructor for class org.intermine.bio.dataconversion.EnsemblIdResolverFactory
Construct without SO term of the feature type.
ensemblIds - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord
 
EnsemblSnpDbConverter - Class in org.intermine.bio.dataconversion
Read Ensembl SNP data directly from MySQL variation database.
EnsemblSnpDbConverter(Database, Model, ItemWriter) - Constructor for class org.intermine.bio.dataconversion.EnsemblSnpDbConverter
Construct a new EnsemblSnpDbConverter.
EnsembSnpLoaderTask - Class in org.intermine.bio.dataconversion
Reworked version of GFF converter for GVF files
EnsembSnpLoaderTask() - Constructor for class org.intermine.bio.dataconversion.EnsembSnpLoaderTask
 
ensureBagIsDeleted(Profile, String) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils
After this method returns, the will be no bag with the given name in the given profile.
entrez - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord
 
EntrezGeneIdResolverFactory - Class in org.intermine.bio.dataconversion
ID resolver for Entrez genes.
EntrezGeneIdResolverFactory() - Constructor for class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
Constructor read pid configuration
EntrezOrganismRetriever - Class in org.intermine.bio.dataconversion
Class to fill in organism information using Entrez.
EntrezOrganismRetriever() - Constructor for class org.intermine.bio.dataconversion.EntrezOrganismRetriever
 
EntrezPublicationsRetriever - Class in org.intermine.bio.dataconversion
Class to fill in all publication information from pubmed
EntrezPublicationsRetriever() - Constructor for class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
 
entrySet() - Method in class org.intermine.api.profile.UserPreferences
 
entrySet() - Method in class org.intermine.api.util.DevNullMap
 
entrySet() - Method in class org.intermine.util.AlwaysMap
entrySet() - Method in class org.intermine.util.IdentityMap
entrySet() - Method in class org.intermine.util.ReferenceMap
entrySet() - Method in class org.intermine.webservice.client.results.JsonRowMap
 
entrySet() - Method in class org.intermine.webservice.client.results.ResultRowMap
 
eof - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
eq(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be equal to a value.
EQ - Static variable in class org.intermine.sql.query.Constraint
An operation for this constraint indicating that left is equal to right.
EQUAL - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes one constraint as being equal to another constraint.
EQUAL - Static variable in class org.intermine.sql.query.AbstractValue
Describes two AbstractValues as being equal.
equals(Object) - Method in class org.intermine.api.bag.BagQueryResult.IssueResult
equals(Object) - Method in class org.intermine.api.bag.SharingInvite
 
equals(Object) - Method in class org.intermine.api.beans.ObjectDetails
 
equals(Object) - Method in class org.intermine.api.beans.PartnerLink
 
equals(Object) - Method in class org.intermine.api.idresolution.ResolutionJob
 
equals(Object) - Method in class org.intermine.api.mines.ObjectRequest
 
equals(Object) - Method in class org.intermine.api.profile.BagValue
Two bag values are identical if they have the same value and extra value.
equals(Object) - Method in class org.intermine.api.profile.SavedQuery
Test receiver for equality with passed object.
equals(Object) - Method in class org.intermine.api.results.Column
equals(Object) - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
equals(Object) - Method in class org.intermine.api.results.flatouterjoins.MultiRowLaterValue
equals(Object) - Method in class org.intermine.api.results.ResultElement
equals(Object) - Method in class org.intermine.api.template.ApiTemplate
 
equals(Object) - Method in class org.intermine.bio.chado.ChadoCVTerm
equals(Object) - Method in class org.intermine.bio.ontology.OboTermSynonym
equals(Object) - Method in class org.intermine.bio.util.OrganismData
equals(Object) - Method in class org.intermine.bio.web.model.GenomicRegion
 
equals(Object) - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint
 
equals(Object) - Method in class org.intermine.metadata.AttributeDescriptor
equals(Object) - Method in class org.intermine.metadata.ClassDescriptor
equals(Object) - Method in class org.intermine.metadata.CollectionDescriptor
EQUALS - Static variable in class org.intermine.metadata.ConstraintOp
Require that the two arguments are equal, regardless of case for strings
equals(Object) - Method in class org.intermine.metadata.Model
equals(Object) - Method in class org.intermine.metadata.PrimaryKey
equals(Object) - Method in class org.intermine.metadata.ReferenceDescriptor
equals(Object) - Method in class org.intermine.metadata.StringUtil.LineWrappedString
equals(Object, Object) - Static method in class org.intermine.metadata.Util
Compare two objects, using their .equals method, but comparing null to null as equal.
equals(Object) - Method in class org.intermine.objectstore.query.BagConstraint
equals(Object) - Method in class org.intermine.objectstore.query.ClassConstraint
Tests whether two ClassConstraints are equal.
equals(Object) - Method in class org.intermine.objectstore.query.Clob
Override Object#equals.
equals(Object) - Method in class org.intermine.objectstore.query.ConstraintSet
Test whether two ConstraintSets are equal, overrides Object.equals().
equals(Object) - Method in class org.intermine.objectstore.query.ContainsConstraint
Test whether two ContainsConstraints are equal, overrides Object.equals()
equals(Object) - Method in class org.intermine.objectstore.query.iql.IqlQuery
equals(Object) - Method in class org.intermine.objectstore.query.MultipleInBagConstraint
equals(Object) - Method in class org.intermine.objectstore.query.ObjectStoreBag
Override Object#equals.
equals(Object) - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
equals(Object) - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject
equals(Object) - Method in class org.intermine.objectstore.query.OverlapConstraint
equals(Object) - Method in class org.intermine.objectstore.query.PathExpressionField
equals(Object) - Method in class org.intermine.objectstore.query.QueryCast
equals(Object) - Method in class org.intermine.objectstore.query.QueryField
Returns true if this is equal to the given object.
equals(Object) - Method in class org.intermine.objectstore.query.QueryValue
Overrides Object.
equals(Object) - Method in class org.intermine.objectstore.query.Results
 
equals(Object) - Method in class org.intermine.objectstore.query.ResultsInfo
equals(Object) - Method in class org.intermine.objectstore.query.SimpleConstraint
Test whether two SimpleConstraints are equal, overrides Object.equals()
equals(Object) - Method in class org.intermine.objectstore.query.SubqueryConstraint
Test whether two SubqueryConstraints are equal, overrides Object.equals()
equals(Object) - Method in class org.intermine.objectstore.query.SubqueryExistsConstraint
Test whether two SubqueryConstraints are equal, overrides Object.equals()
equals(Object) - Method in class org.intermine.pathquery.LogicExpression
equals(Object) - Method in class org.intermine.pathquery.Node
equals(Object) - Method in class org.intermine.pathquery.OrderElement
equals(Object) - Method in class org.intermine.pathquery.Path
equals(Object) - Method in class org.intermine.pathquery.PathQuery
 
equals(Object) - Method in class org.intermine.sql.precompute.PrecomputedTable
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.AbstractConstraint
Overrides Object.equals();
equals(Object) - Method in class org.intermine.sql.query.AbstractTable
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.AbstractValue
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.Constant
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.ExplainResult
equals(Object) - Method in class org.intermine.sql.query.Field
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.Function
Overrides Object.equals.
equals(Object) - Method in class org.intermine.sql.query.OrderDescending
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.Query
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.SelectValue
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.SubQuery
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.Table
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.writebatch.Row
equals(Object) - Method in class org.intermine.template.TemplateQuery
 
equals(Object) - Method in class org.intermine.util.AlwaysMap
equals(Object) - Method in class org.intermine.util.IdentityMap
equals(Object) - Method in class org.intermine.util.ReferenceMap
equals(Object) - Method in class org.intermine.web.logic.config.Displayer
equals(Object) - Method in class org.intermine.web.logic.config.FieldConfig
equals(Object) - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart
 
equals(Object) - Method in class org.intermine.web.logic.config.TableExportConfig
equals(Object) - Method in class org.intermine.web.logic.config.Type
equals(Object) - Method in class org.intermine.web.logic.config.WebConfig
equals(Object) - Method in class org.intermine.web.logic.template.ConstraintInput
 
equals(Object) - Method in class org.intermine.web.logic.TreeNode
equals(Object) - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
 
equals(Object) - Method in class org.intermine.webservice.client.results.Item
Determine whether this object is equal to the other.
equals(Object) - Method in class org.intermine.webservice.client.results.Page
 
equals(Object) - Method in class org.intermine.webservice.server.core.Either
 
equals(Object) - Method in class org.intermine.webservice.server.jbrowse.Command
 
equals(Object) - Method in class org.intermine.webservice.server.jbrowse.Segment
 
equals(Object) - Method in class org.intermine.webservice.server.JWTBuilder
 
equals(Object) - Method in class org.intermine.xml.full.Attribute
equals(Object) - Method in class org.intermine.xml.full.Item
equals(Object) - Method in class org.intermine.xml.full.Reference
equals(Object) - Method in class org.intermine.xml.full.ReferenceList
equalsExactly(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be exactly equal to a value.
equalsIgnoreAlias(AbstractTable) - Method in class org.intermine.sql.query.AbstractTable
Compare this AbstractTable to another, ignoring little details like aliases.
equalsIgnoreAlias(AbstractTable) - Method in class org.intermine.sql.query.SubQuery
Compare this SubQuery to another AbstractTable, ignoring alias.
equalsIgnoreAlias(AbstractTable) - Method in class org.intermine.sql.query.Table
Compare this Table to another AbstractTable, ignoring alias.
equalsNoUnion(Object) - Method in class org.intermine.sql.query.Query
Returns true if this Query is equivalent to obj, disregarding other queries in the UNION.
equalsOnlyAlias(AbstractTable) - Method in class org.intermine.sql.query.AbstractTable
Compare this AbstractTable to another, only comparing the alias.
equalsTableOnlyAlias(AbstractValue) - Method in class org.intermine.sql.query.Field
Compare this Field to another AbstractValue, including only the table alias.
equalToLoop(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be equal to a loopPath.
EquivalentObjectFetcher - Interface in org.intermine.dataloader
Interface providing methods to look up equivalent objects by primary key in a production objectstore.
EquivalentObjectHints - Class in org.intermine.dataloader
Object for holding hint data for the getEquivalentObjects method in IntegrationWriters.
EquivalentObjectHints(ObjectStore) - Constructor for class org.intermine.dataloader.EquivalentObjectHints
Constructor.
equivalents - Variable in class org.intermine.dataloader.BatchingFetcher
 
error(SAXParseException) - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler
}
ERROR_CODE - Static variable in exception org.intermine.webservice.client.exceptions.ServiceException
 
ERROR_INTRO - Static variable in class org.intermine.webservice.server.output.FlatFileFormatter
The string that begins an error line.
ERROR_INTRO - Static variable in class org.intermine.webservice.server.output.PlainFormatter
The string that begins an error line.
ERROR_UPGRADER - Static variable in interface org.intermine.api.bag.IdUpgrader
An upgrader that always fails.
ErrorCorrection - Class in org.intermine.web.logic.widget
See online help docs for detailed description of what error correction is and why we need it.
ErrorCorrection.Strategy - Enum in org.intermine.web.logic.widget
 
ErrorMessageParser - Class in org.intermine.webservice.client.util
Parses service error message.
ErrorMessagesController - Class in org.intermine.web.struts
Take the messages stored in the session which are not using ActionMessages or ActionErrors and put them in the request
ErrorMessagesController() - Constructor for class org.intermine.web.struts.ErrorMessagesController
 
ERRORS - Static variable in class org.intermine.web.logic.Constants
Session attribute that temporarily holds a Vector of errors that will be displayed by the errorMessages.jsp on the next page viewed by the user and then removed (allows errors after redirect).
escapeAttribute(Object) - Method in class org.intermine.webservice.server.output.XMLFormatter
 
escapeBackslash(String) - Static method in class org.intermine.metadata.StringUtil
Escape single backslash with single forwardslash for correct storage in postgres.
escapeElementContent(String) - Method in class org.intermine.webservice.server.output.XMLFormatter
Escape the content of an element.
escapeReservedWord(String) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Converts words into escaped form.
escapeWithBackslashes(String) - Static method in class org.intermine.metadata.StringUtil
Escapes single quotes and backslashes, with backslashes.
estimate(Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Explain a Query (give estimate for execution time and number of rows).
estimate(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Explain a Query (give estimate for execution time and number of rows).
estimate(Query) - Method in interface org.intermine.objectstore.ObjectStore
Explain a Query (give estimate for execution time and number of rows).
estimate(Query) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Explain a Query (give estimate for execution time and number of rows).
ESTIMATE - Static variable in class org.intermine.objectstore.query.ResultsInfo
Denotes that the result of getRows() is a pure estimate that is not contradicted by the min or max
estimate(Query) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Explain a Query (give estimate for execution time and number of rows).
estimate(Query) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Explain a Query (give estimate for execution time and number of rows).
estimatedRows - Variable in class org.intermine.sql.query.ExplainResult
 
estimateWithConnection(Connection, Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Runs an EXPLAIN for the given query.
ESUMMARY_URL - Static variable in class org.intermine.bio.dataconversion.EntrezOrganismRetriever
 
ESUMMARY_URL - Static variable in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
 
EsynDisplayer - Class in org.intermine.bio.web.displayer
displayer for esyn
EsynDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.EsynDisplayer
Construct with config and the InterMineAPI.
EsynListDisplayer - Class in org.intermine.bio.web
displayer for esyn on list analysis page
EsynListDisplayer() - Constructor for class org.intermine.bio.web.EsynListDisplayer
 
evaluate(String) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.StainingLevelEvaluator
String representing the level to integer conversion
everOptimise() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Returns whether optimisation should be permitted.
everOptimise() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Returns whether optimisation should be permitted.
evictFromCache(Profile) - Method in class org.intermine.api.profile.ProfileManager
Remove a profile from the cache
EvictOrphansTask - Class in org.intermine.web.task
A task for removing tags that don't point to anything.
EvictOrphansTask() - Constructor for class org.intermine.web.task.EvictOrphansTask
 
evidence - Variable in class org.intermine.bio.dataconversion.UniprotEntry.Comment
 
EXACT_MATCH - Static variable in class org.intermine.metadata.ConstraintOp
Require that the two arguments are exactly equal
EXCEPT - Static variable in class org.intermine.objectstore.query.ObjectStoreBagCombination
Constant representing an EXCEPT operation
EXCLUDES - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints as being mutually exclusive.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.flymine.web.ChartRenderer
First, check for a cached image, otherwise defer to appropriate method.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.flymine.web.GeneMicroArrayDisplayerController
execute(PathQuery) - Method in class org.intermine.api.query.PathQueryExecutor
Executes object store query and returns results as iterator over rows.
execute(PathQuery, int, int) - Method in class org.intermine.api.query.PathQueryExecutor
Executes object store query and returns results as iterator over rows.
execute(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor
Create and ObjectStore query from a PathQuery and execute it, returning results in a format appropriate for displaying a web table.
execute(PathQuery, Map<String, BagQueryResult>) - Method in class org.intermine.api.query.WebResultsExecutor
Create and ObjectStore query from a PathQuery and execute it, returning results in a format appropriate for displaying a web table.
execute() - Method in class org.intermine.bio.dataconversion.EnsembSnpLoaderTask
 
execute() - Method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever
For each Organism in the objectstore, retreive it's details from entrez using the taxon and fill in the details in the organism object.
execute() - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
Synchronize publications with pubmed using pmid
execute() - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
 
execute() - Method in class org.intermine.bio.dataconversion.UniprotFilterTask
execute() - Method in class org.intermine.bio.dataconversion.VcfLoaderTask
 
execute() - Method in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask
Use the linkFile attribute (which is a file containing FlyBase Translation <-> UniProt accession numbers) to link Translation objects to Protein objects in the ObjectStoreWriter.
execute() - Method in class org.intermine.bio.postprocess.PostProcessOperationsTask
execute() - Method in class org.intermine.bio.task.GFF3ConverterTask
 
execute() - Method in class org.intermine.bio.task.OboConverterTask
Run the task
execute() - Method in class org.intermine.bio.task.SOClassNameMapMakerTask
execute() - Method in class org.intermine.bio.task.SOToModelTask
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.AttributeLinksController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.EsynListDisplayer
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.FriendlyMineLinkController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.OtherMinesLinkController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.GalaxyExportAction
 
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.GalaxyExportOptionsController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.GenomicRegionSearchAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.GenomicRegionSearchAjaxAction
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.GenomicRegionSearchOptionsController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.SequenceExportAction
This action is invoked directly to export SequenceFeatures.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.SequenceExportOptionsController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.SequenceFeatureExportOptionsController
execute() - Method in class org.intermine.bio.webservice.BioQueryService
 
execute(Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Execute a Query on this ObjectStore
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute() - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
execute() - Method in class org.intermine.dataloader.XmlDataLoaderTask
execute(Query) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Execute a Query on this ObjectStore
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute(Query) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Execute a Query on this ObjectStore
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Execute a Query on this ObjectStore
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Execute a Query on this ObjectStore
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute() - Method in class org.intermine.objectstore.intermine.TorqueModelOutputTask
execute(Query) - Method in interface org.intermine.objectstore.ObjectStore
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in interface org.intermine.objectstore.ObjectStore
Execute a Query on this ObjectStore
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in interface org.intermine.objectstore.ObjectStore
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute(Query) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Execute a Query on this ObjectStore
execute(Query) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Execute a Query on this ObjectStore
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute(Query) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Execute a Query on this ObjectStore
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute() - Method in class org.intermine.task.AcceptanceTestTask
 
execute() - Method in class org.intermine.task.AnalyseDbTask
execute() - Method in class org.intermine.task.BuildDbTask
execute() - Method in class org.intermine.task.CreateIndexesTask
execute(Connection, String) - Method in class org.intermine.task.CreateIndexesTask
Execute an sql statement.
execute() - Method in class org.intermine.task.CreatePropertiesFile
execute
execute() - Method in class org.intermine.task.DBConverterTask
Run the task
execute() - Method in class org.intermine.task.Dependencies
Execute the task.
execute() - Method in class org.intermine.task.DirectDataLoaderTask
 
execute() - Method in class org.intermine.task.DirectoryConverterTask
Run the task.
execute() - Method in class org.intermine.task.DropPrecomputedTablesTask
execute() - Method in class org.intermine.task.FileConverterTask
Run the task
execute() - Method in class org.intermine.task.FileName
 
execute() - Method in class org.intermine.task.FullXmlConverterTask
execute() - Method in class org.intermine.task.GrantTask
execute() - Method in class org.intermine.task.InheritanceDotTask
execute() - Method in class org.intermine.task.Integrate
Run the integration.
execute() - Method in class org.intermine.task.MergeSourceModelsTask
execute() - Method in class org.intermine.task.ModelMergerTask
execute() - Method in class org.intermine.task.ModelOutputTask
execute() - Method in class org.intermine.task.PostProcessorTask
Run the task
execute() - Method in class org.intermine.task.PostProcessTask
execute() - Method in class org.intermine.task.PrecomputeTask
execute() - Method in class org.intermine.task.ReadResourceTask
Execute the task to set a property from a resource.
execute() - Method in class org.intermine.task.RetrieveMetadataTask
execute() - Method in class org.intermine.task.RunIqlQueryTask
execute() - Method in class org.intermine.task.SetDeployURL
 
execute() - Method in class org.intermine.task.StaticMethodTask
 
execute() - Method in class org.intermine.task.StoreMetadataTask
execute() - Method in class org.intermine.task.SummariseObjectStoreTask
execute() - Method in class org.intermine.task.XPathSelect
Execute the task.
execute(HttpServletRequest, ReportObject) - Method in class org.intermine.web.displayer.ReportDisplayer
Execute is called for each report page with the object to be displayed.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.AddColumnAction
Executes action.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.AddToBagAction
Save a single object to an existing bag.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ApiJavaController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ApiPerlController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.AspectController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.AvailableColumnsController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagBuildController
Set up environment for the buildBag page.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagDetailsAction
Set up session attributes for the bag details page.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagDetailsController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagUpgradeAction
Action for creating BagQueryResult for a specific bag not yet current
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagUploadConfirmAction
Action to save a bag from the bagUploadConfirm page into the user profile.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagUploadConfirmController
Set up the bagUploadConfirm page.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagUploadConfirmIssueController
Initialise attributes for the bagUploadConfirmIssue.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BeginAction
Either display the query builder or redirect to project.sitePrefix.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BuildBagAction
Action for creating a bag of InterMineObjects or Strings from identifiers in text field.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangePasswordAction
Method called when user has finished filling out the 'change password' form
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableSizeAction
 
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ClassChooserController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CollectionDetailsAction
Create PagedTable for this collection, register it with an identifier and redirect to results.do?
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CollectionTableAction
Create PagedTable for this collection, register it with an identifier
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ContactAction
Method called when user has submitted valid feedback form
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ConvertBagController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CountTableController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CreateAccountAction
Method called when user has finished updating a constraint.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CreateTemplateAction
Take the current query and TemplateBuildState from the session and create a TemplateQuery.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CurrentQueryAction
Either display the query builder or redirect to project.sitePrefix.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.EditPropertiesAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.EditTemplateAction
Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ErrorMessagesController
 
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ExportController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ExportOptionsController
Set up the exportOptions tile.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ExportQueryAction
Method called to export a saved Query.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ExportTagsAction
Export user's tags.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.FavouritesController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.FileDownloadAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.FindInListAction
Method called when user has submitted the search form.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.GetAttributeAsFileAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.GotoWebSearchableAction
Method called when user has submitted search form.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.HeartbeatAction
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.HintsController
 
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.HtmlHeadController
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ImportQueriesAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ImportTagsAction
Import user's tags.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.InlineTagEditorController
execute(Exception, ExceptionConfig, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.InterMineExceptionHandler
Handle the exception.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.InvitationAction
 
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.KeywordSearchResultsController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LabelsSummaryAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoginAction
Method called for login in
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoginController
Set up the form for login.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LogoutAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyBagAction
Forward to the correct method based on the button pressed
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyBagDetailsAction
Forward to the correct method based on the button pressed
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryAction
Forward to the correct method based on the button pressed.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifySuperUserAction
Forward to the correct method based on the button pressed
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyTemplateAction
Forward to the correct method based on the button pressed.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.MyMineController
Set up attributes for the myMine page.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.oauth2.Authenticator
Method called for login in
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.oauth2.Callback
Method called for login in
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ObjectTrailController
Looks at the "trail" request parameter and extracts the object ids from it, then looks up the actual objects and creates a list of TrailItems.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ObjectViewController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.PasswordResetAction
Method called when the form is submitted.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.PasswordResetController
Set up the form.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.PollQueryAction
Handle request from client.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.PortalQueryAction
Link-ins from other sites end up here (after some redirection).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderConstraintAction
Method called when user has finished updating a constraint.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderConstraintController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderSummaryController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderViewAction
Run the query and forward to the results page.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryClassSelectAction
Add a QueryClass of a specified type to the current query.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ReportAspectController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ReportController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ReportDisplayerController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ReportInListController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ReportTemplateController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.RequestPasswordAction
Method called when user has finished updating a constraint
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ResultsAction
Called before results table is rendered.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.RunQueryAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SaveBagAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SaveFromIdsToBagAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SaveQueryAction
Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SharingBagUsersController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SubMenuController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SummariseTemplatesAction
Summarises every public template, and then forwards to the mymine template page.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TableController
Set up table tile.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TableExportAction
Method called to export a PagedTable object.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplateAction
Build a query based on the template and the input from the user.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplateController
Finds the correct template to display in the following ways: First, looks for a "name" request parameter and uses that for a the lookup.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplateListController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplateProblemsController
Called before template problem page is rendered.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplatesController
Set up attributes for the templates page.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplatesExportAction
Build a query based on the template and the input from the user.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplatesImportAction
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TreeController
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TriageBagAction
Forward to the correct method based on the button pressed
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.UsersController
 
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.WebSearchableListController
Set up the attributes for webSearchableList.tile
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.WebserviceCodeGenAction
 
execute() - Method in class org.intermine.web.task.CreateSearchIndexTask
 
execute() - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
Write templates and tags to a file.
execute() - Method in class org.intermine.web.task.EvictOrphansTask
 
execute() - Method in class org.intermine.web.task.IssueTokenTask
 
execute() - Method in class org.intermine.web.task.LoadBagValuesTask
Execute the task - load bagvalues table.
execute() - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
Load templates from an xml file into a userprofile account.
execute() - Method in class org.intermine.web.task.ModelUpdateTask
Update savedquery, savedtemplatequery and savedbag in the userprofile through ModelUpdate object
execute() - Method in class org.intermine.web.task.PrecomputeTemplatesTask
execute() - Method in class org.intermine.web.task.ProfileReadTask
Execute the task - read the profiles.
execute() - Method in class org.intermine.web.task.ProfileWriteTask
Execute the task - write the profiles as XML.
execute() - Method in class org.intermine.web.task.TemplateTrackReadTask
Execute the task - read the profiles.
execute() - Method in class org.intermine.web.task.TemplateTrackWriteTask
Execute the task - write the template tracks as XML.
execute() - Method in class org.intermine.web.task.UpdateListTablesTask
Execute the task.
execute() - Method in class org.intermine.web.task.UpdateTrackTableTask
Execute the task - read the profiles.
execute() - Method in class org.intermine.web.task.VerifyTokenTask
 
execute() - Method in class org.intermine.webservice.server.branding.BrandingService
 
execute() - Method in class org.intermine.webservice.server.ClassKeysService
 
execute() - Method in class org.intermine.webservice.server.clob.SequenceService
 
execute() - Method in class org.intermine.webservice.server.complexes.ExportService
 
execute() - Method in class org.intermine.webservice.server.data.DataService
 
execute() - Method in class org.intermine.webservice.server.idresolution.IdResolutionService
 
execute() - Method in class org.intermine.webservice.server.idresolution.JobRemovalService
 
execute() - Method in class org.intermine.webservice.server.idresolution.JobResultsService
 
execute() - Method in class org.intermine.webservice.server.idresolution.JobStatusService
 
execute() - Method in class org.intermine.webservice.server.jbrowse.Config
 
execute() - Method in class org.intermine.webservice.server.jbrowse.Endpoint
 
execute() - Method in class org.intermine.webservice.server.jbrowse.Names
 
execute() - Method in class org.intermine.webservice.server.lists.AvailableListsService
 
execute() - Method in class org.intermine.webservice.server.lists.ListDeletionService
 
execute() - Method in class org.intermine.webservice.server.lists.ListMakerService
 
execute() - Method in class org.intermine.webservice.server.lists.ListRenameService
 
execute() - Method in class org.intermine.webservice.server.lists.ListShareCreationService
Runs service.
execute() - Method in class org.intermine.webservice.server.lists.ListShareDeletionService
 
execute() - Method in class org.intermine.webservice.server.lists.ListShareDetailsService
 
execute() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationAcceptanceService
 
execute() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationDeletionService
 
execute() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationDetailsService
 
execute() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationService
 
execute() - Method in class org.intermine.webservice.server.lists.ListTagAddingService
 
execute() - Method in class org.intermine.webservice.server.lists.ListTagService
 
execute() - Method in class org.intermine.webservice.server.model.ModelService
Runs service.
execute() - Method in class org.intermine.webservice.server.path.PossibleValuesService
 
execute() - Method in class org.intermine.webservice.server.query.CodeService
 
execute() - Method in class org.intermine.webservice.server.query.QueryRemovalService
 
execute() - Method in class org.intermine.webservice.server.query.QueryRetrieverService
 
execute() - Method in class org.intermine.webservice.server.query.QueryStoreService
 
execute() - Method in class org.intermine.webservice.server.query.QueryToListService
 
execute() - Method in class org.intermine.webservice.server.query.QueryUploadService
 
execute() - Method in class org.intermine.webservice.server.query.result.QueryResultService
Executes service specific logic.
execute() - Method in class org.intermine.webservice.server.query.SavedQueryRetrievalService
 
execute() - Method in class org.intermine.webservice.server.SchemaListService
 
execute() - Method in class org.intermine.webservice.server.search.QuickSearch
 
execute() - Method in class org.intermine.webservice.server.SessionService
 
execute() - Method in class org.intermine.webservice.server.SummaryService
 
execute() - Method in class org.intermine.webservice.server.template.AvailableTemplatesService
 
execute() - Method in class org.intermine.webservice.server.template.result.TemplateResultService
Executes service specific logic.
execute() - Method in class org.intermine.webservice.server.template.SingleTemplateService
 
execute() - Method in class org.intermine.webservice.server.template.TemplateRemovalService
 
execute() - Method in class org.intermine.webservice.server.template.TemplateUploadService
 
execute() - Method in class org.intermine.webservice.server.user.DeletePreferencesService
 
execute() - Method in class org.intermine.webservice.server.user.DeleteTokensService
 
execute() - Method in class org.intermine.webservice.server.user.DeletionTokenCancellationService
 
execute() - Method in class org.intermine.webservice.server.user.DeletionTokenInfoService
 
execute() - Method in class org.intermine.webservice.server.user.DeregistrationService
 
execute() - Method in class org.intermine.webservice.server.user.NewDeletionTokenService
 
execute() - Method in class org.intermine.webservice.server.user.NewUserService
 
execute() - Method in class org.intermine.webservice.server.user.PermaTokenDeletionService
 
execute() - Method in class org.intermine.webservice.server.user.PermaTokenInfoService
 
execute() - Method in class org.intermine.webservice.server.user.ReadPreferencesService
 
execute() - Method in class org.intermine.webservice.server.user.SetPreferencesService
 
execute() - Method in class org.intermine.webservice.server.user.TokenService
 
execute() - Method in class org.intermine.webservice.server.user.TokensService
 
execute() - Method in class org.intermine.webservice.server.user.WhoAmIService
 
execute() - Method in class org.intermine.webservice.server.VersionService
 
execute() - Method in class org.intermine.webservice.server.WebService
Runs service.
execute() - Method in class org.intermine.webservice.server.widget.AvailableWidgetsService
 
execute() - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService
Executes service specific logic.
execute() - Method in class org.intermine.webservice.server.widget.GraphService
 
execute() - Method in class org.intermine.webservice.server.widget.TableWidgetService
 
executeRequest(Request) - Method in class org.intermine.webservice.client.core.Service
Open connection and returns connection.
executeSingleton(Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query) - Method in interface org.intermine.objectstore.ObjectStore
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in interface org.intermine.objectstore.ObjectStore
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSqlInParallel(String) - Method in class org.intermine.sql.Database
Executes an SQL statement on the database in a separate thread.
executeWithConnection(Connection, Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Performs the actual execute, given a Connection.
executeWithConnection(Connection, Query, int, int, boolean, boolean, Map<Object, Integer>, Set<PrecomputedTable>, OptimiserCache) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Performs the actual execute, given a Connection.
existingBagName - Variable in class org.intermine.web.struts.ModifyBagDetailsForm
 
existingBagName - Variable in class org.intermine.web.struts.SaveBagForm
 
EXISTS - Static variable in class org.intermine.metadata.ConstraintOp
Subquery exists
exists() - Method in class org.intermine.objectstore.intermine.CheckForIsNotNullConstraint
Check whether a NOT NULL constraint was found.
expand(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TreeAction
Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
expandPath(ObjectStore, String) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil
Given a path return a set of paths replacing a path with a '+' preceding a class name with an additional path for every subclass of that class.
expandVars(String, Map) - Method in class org.intermine.task.CreatePropertiesFile
 
experimentRefId - Variable in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder
 
EXPIRE_INTERVAL - Static variable in class org.intermine.sql.precompute.OptimiserCache
Number of events to happen before an expiration run.
ExpiresHeaderFilter - Class in org.intermine.web.filters
A Filter that modifies response headers of outgoing pages.
ExpiresHeaderFilter() - Constructor for class org.intermine.web.filters.ExpiresHeaderFilter
 
explain(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor
Explain a query and return estimates of execution time and row count.
explain - Variable in class org.intermine.objectstore.query.Results
 
explain - Variable in class org.intermine.sql.query.Query
 
explainResult - Variable in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
 
ExplainResult - Class in org.intermine.sql.query
Represents a result from an EXPLAIN request to a database.
ExplainResult() - Constructor for class org.intermine.sql.query.ExplainResult
 
export(Iterator<? extends List<ResultElement>>) - Method in class org.intermine.bio.web.export.BEDExporter
 
export(Iterator<? extends List<ResultElement>>, Collection<Path>, Collection<Path>) - Method in class org.intermine.bio.web.export.BEDExporter
 
export(PagedTable, HttpServletRequest, HttpServletResponse, TableExportForm, Collection<Path>, Collection<Path>) - Method in class org.intermine.bio.web.export.BEDHttpExporter
Method called to export a PagedTable object as BED.
export(Iterator<? extends List<ResultElement>>, Collection<Path>, Collection<Path>) - Method in class org.intermine.bio.web.export.GAFExporter
 
export(Iterator<? extends List<ResultElement>>) - Method in class org.intermine.bio.web.export.GAFExporter
 
export(List<GenomicRegion>) - Method in class org.intermine.bio.web.export.GenomicRegionSequenceExporter
DO export
export(Iterator<? extends List<ResultElement>>, Collection<Path>, Collection<Path>) - Method in class org.intermine.bio.web.export.GFF3Exporter
Do export.
export(Iterator<? extends List<ResultElement>>) - Method in class org.intermine.bio.web.export.GFF3Exporter
 
export(PagedTable, HttpServletRequest, HttpServletResponse, TableExportForm, Collection<Path>, Collection<Path>) - Method in class org.intermine.bio.web.export.GFF3HttpExporter
Method called to export a PagedTable object as GFF3.
export(Iterator<? extends List<ResultElement>>) - Method in class org.intermine.bio.web.export.SequenceExporter
 
export(Iterator<? extends List<ResultElement>>, Collection<Path>, Collection<Path>) - Method in class org.intermine.bio.web.export.SequenceExporter
Do export.
export(PagedTable, HttpServletRequest, HttpServletResponse, TableExportForm, Collection<Path>, Collection<Path>) - Method in class org.intermine.bio.web.export.SequenceHttpExporter
Method called to export a PagedTable object using the BioJava sequence and feature writers.
export(PathQuery, Profile) - Method in class org.intermine.bio.webservice.AbstractRegionExportService
Method that carries out the logic for this exporter.
export(PagedTable, HttpServletRequest, HttpServletResponse, TableExportForm, Collection<Path>, Collection<Path>) - Method in class org.intermine.model.testmodel.web.EmployeeExporter
Method called to export a RESULTS_TABLE containing an Employee by writing it to the OutputStream of the Response.
export(Iterator<? extends List<ResultElement>>, Collection<Path>, Collection<Path>) - Method in interface org.intermine.web.logic.export.Exporter
Do export.
export(Iterator<? extends List<ResultElement>>) - Method in interface org.intermine.web.logic.export.Exporter
Perform the export with the exporter's defaults in the absence of path collection changes.
export(Iterator<? extends List<ResultElement>>, Collection<Path>, Collection<Path>) - Method in class org.intermine.web.logic.export.ExporterImpl
Do export.
export(Iterator<? extends List<ResultElement>>) - Method in class org.intermine.web.logic.export.ExporterImpl
 
export(PagedTable, HttpServletRequest, HttpServletResponse, TableExportForm, Collection<Path>, Collection<Path>) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter
Perform export.
export(PagedTable, HttpServletRequest, HttpServletResponse, TableExportForm, Collection<Path>, Collection<Path>) - Method in interface org.intermine.web.logic.export.http.TableHttpExporter
Method called to export a PagedTable object
export(List<List<String>>) - Method in class org.intermine.web.logic.export.string.StringTableExporter
Perform export.
export(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoadTemplateAction
Load a template from template name passed as parameter.
export(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryAction
Export the selected queries
export(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyTemplateAction
Export the selected templates.
ExportController - Class in org.intermine.web.struts
Controller to initialise for the export.tile
ExportController() - Constructor for class org.intermine.web.struts.ExportController
 
Exporter - Interface in org.intermine.web.logic.export
Simple exporter interface.
ExporterImpl - Class in org.intermine.web.logic.export
Simple exporter exporting data as tab separated, comma separated and so.
ExporterImpl(OutputStream, RowFormatter) - Constructor for class org.intermine.web.logic.export.ExporterImpl
Constructor.
ExporterImpl(OutputStream, RowFormatter, String, List<String>) - Constructor for class org.intermine.web.logic.export.ExporterImpl
Constructor.
ExportException - Exception in org.intermine.web.logic.export
Exception thrown if the there is a problem while exporting (eg. from FieldExporter)
ExportException(String) - Constructor for exception org.intermine.web.logic.export.ExportException
Create a new ExportException.
ExportException(String, Exception) - Constructor for exception org.intermine.web.logic.export.ExportException
Create a new ExportException.
exportField(InterMineObject, String, ObjectStore, HttpServletResponse) - Method in class org.intermine.bio.web.export.ResidueFieldExporter
Export a field containing residues in FASTA format.
exportField(InterMineObject, String, ObjectStore, HttpServletResponse) - Method in class org.intermine.model.testmodel.web.CommaFieldExporter
Example FieldExporter that splits the a String field at the first comma and outputs each bit on a new line.
exportField(InterMineObject, String, ObjectStore, HttpServletResponse) - Method in interface org.intermine.web.logic.export.FieldExporter
Example FieldExporter that splits the a String field at the first comma and outputs each bit on a new line.
ExportHelper - Class in org.intermine.web.logic.export
Helper methods for exporters.
ExportOptionsController - Class in org.intermine.web.struts
Controller for exportOptions.tile
ExportOptionsController() - Constructor for class org.intermine.web.struts.ExportOptionsController
 
ExportQueryAction - Class in org.intermine.web.struts
Export the current query in XML format.
ExportQueryAction() - Constructor for class org.intermine.web.struts.ExportQueryAction
 
ExportResultsIterator - Class in org.intermine.api.results
An Iterator that produces data in a format suitable for exporting.
ExportResultsIterator(PathQuery, Query, Results, Map<String, QuerySelectable>) - Constructor for class org.intermine.api.results.ExportResultsIterator
Constructor for ExportResultsIterator.
ExportService - Class in org.intermine.webservice.server.complexes
Web service that produces JSON required by the complex viewer.
ExportService(InterMineAPI) - Constructor for class org.intermine.webservice.server.complexes.ExportService
Default constructor.
ExportService.FeatureHolder - Class in org.intermine.webservice.server.complexes
hold the feature / linked feature relationships here
ExportService.FeatureHolder(String, DefaultModelledParticipant) - Constructor for class org.intermine.webservice.server.complexes.ExportService.FeatureHolder
 
ExportTagsAction - Class in org.intermine.web.struts
Export tags.
ExportTagsAction() - Constructor for class org.intermine.web.struts.ExportTagsAction
 
expression - Variable in class org.intermine.task.XPathSelect
 
EXTRA_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
extra value parameter
EXTRA_VALUE_CONSTRAINT - Static variable in class org.intermine.api.config.Constants
Constrain by an extra value
extraAttribute - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
extraFieldValue - Variable in class org.intermine.web.struts.ModifyBagDetailsForm
 
extraProcessing(Sequence, Sequence, BioEntity, Organism, DataSet) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
Do any extra processing needed for this record (extra attributes, objects, references etc.)
extraProcessing(Sequence, Sequence, BioEntity, Organism, DataSet) - Method in class org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask
Do any extra processing needed for this record (extra attributes, objects, references etc.)
extraProcessing(Connection, Map<Integer, FeatureData>) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
For objects that have primaryIdentifier == null, set the primaryIdentifier to be the uniquename column from chado.
extraProcessing(Sequence, Sequence, BioEntity, Organism, DataSet) - Method in class org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask
Do any extra processing needed for this record (extra attributes, objects, references etc.)
extraProcessing(Connection, Map<Integer, FeatureData>) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Do any extra processing for this database, after all other processing is done
extraProcessing(Connection, Map<Integer, FeatureData>) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Do any extra processing for this database, after all other processing is done
ExtraQueryTime - Class in org.intermine.objectstore.intermine
An object that holds information about extra queries run during the ResultsConverter operation.
ExtraQueryTime() - Constructor for class org.intermine.objectstore.intermine.ExtraQueryTime
Constructor.
extraValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 

F

F<A,B> - Class in org.intermine.webservice.server.core
A type for a function from A -> B.
F() - Constructor for class org.intermine.webservice.server.core.F
 
F.Constant<X,R> - Class in org.intermine.webservice.server.core
An implementation of a constant function.
F.Constant(R) - Constructor for class org.intermine.webservice.server.core.F.Constant
Construct a constant function.
FALSE - Static variable in class org.intermine.objectstore.query.QueryValue
The false value
fanOutCombinations(List<Collection<E>>) - Static method in class org.intermine.util.CollectionUtil
Returns a collection containing all possible combinations of the input values.
FastaListService - Class in org.intermine.bio.webservice
Export a list as FASTA.
FastaListService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.FastaListService
 
FastaListServlet - Class in org.intermine.bio.webservice
 
FastaListServlet() - Constructor for class org.intermine.bio.webservice.FastaListServlet
 
FastaLoaderTask - Class in org.intermine.bio.dataconversion
A task that can read a set of FASTA files and create the corresponding Sequence objects in an ObjectStore.
FastaLoaderTask() - Constructor for class org.intermine.bio.dataconversion.FastaLoaderTask
 
FastaQueryService - Class in org.intermine.bio.webservice
A service for exporting query results as fasta.
FastaQueryService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.FastaQueryService
Constructor.
FastaQueryServlet - Class in org.intermine.bio.webservice
A servlet to hand off to the FASTA-query-service.
FastaQueryServlet() - Constructor for class org.intermine.bio.webservice.FastaQueryServlet
 
FastPathObject - Interface in org.intermine.model
A root interface for all objects that can be stored in a InterMine database.
fastSearch(String, String, int) - Method in class org.intermine.web.autocompletion.LuceneSearchEngine
Perform the search but only return n results.
fatalError(SAXParseException) - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler
}
FavouritesController - Class in org.intermine.web.struts
Controller for the starTemplate tile.
FavouritesController() - Constructor for class org.intermine.web.struts.FavouritesController
 
featureMap - Variable in class org.intermine.bio.dataconversion.SequenceProcessor
 
features(Command) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
features(Command) - Method in class org.intermine.webservice.server.jbrowse.genomic.Engine
 
fetchBatchFromObjectStore(int, boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches
Gets a batch from the ObjectStore.
fetchByIds(ObjectStoreInterMineImpl, Connection, Map<Object, Integer>, Class<?>, Collection<Integer>, ExtraQueryTime) - Static method in class org.intermine.objectstore.intermine.ResultsConverter
Fetches a group of objects from the database by ID.
fetchCollectionPathExpression(ObjectStoreInterMineImpl, Connection, Map<Object, Integer>, Query, QueryCollectionPathExpression, List<ResultsRow<Object>>, boolean, ExtraQueryTime, Set<PrecomputedTable>, OptimiserCache) - Static method in class org.intermine.objectstore.intermine.ResultsConverter
Fetches the QueryCollectionPathExpression data for a query.
fetchGeneModels(Gene, Model) - Static method in class org.intermine.bio.web.model.GeneModelCache
Look up gene models for a particular gene, either fetch from cache or create new gene models for each transcript.
fetchObjectPathExpression(ObjectStoreInterMineImpl, Connection, Map<Object, Integer>, Query, QueryObjectPathExpression, List<ResultsRow<Object>>, boolean, ExtraQueryTime, Set<PrecomputedTable>, OptimiserCache) - Static method in class org.intermine.objectstore.intermine.ResultsConverter
Fetches the contents of a QueryObjectPathExpression for a query.
field - Variable in class org.intermine.api.results.ResultElement
 
Field - Class in org.intermine.sql.query
A representation of a field in a table.
Field(String, AbstractTable) - Constructor for class org.intermine.sql.query.Field
Constructor for this Field object.
FieldConfig - Class in org.intermine.web.logic.config
The webapp configuration for one field of a class.
FieldConfig() - Constructor for class org.intermine.web.logic.config.FieldConfig
 
FieldConfigHelper - Class in org.intermine.web.logic.config
Helper methods for the FieldConfig class.
FieldDescriptor - Class in org.intermine.metadata
Abstract representation of a field within a class - could be an attribute, an object reference or a collection.
FieldDescriptor(String) - Constructor for class org.intermine.metadata.FieldDescriptor
Construct, name of field must not be null and must be a valid Java variable name.
FieldExporter - Interface in org.intermine.web.logic.export
An interface implemented by objects that can export the value of a particular.
fieldIsPrimaryKey(Model, Class<?>, String, Source) - Static method in class org.intermine.dataloader.DataLoaderHelper
Returns true if the given field is a member of any primary key on the given class, for the given source.
fieldName - Variable in class org.intermine.objectstore.query.QueryForeignKey
 
fieldName - Variable in class org.intermine.objectstore.query.QueryReference
 
fields - Variable in class org.intermine.sql.logging.DatabaseWriter
 
file - Variable in class org.intermine.codegen.JavaModelOutput
 
file - Variable in class org.intermine.dataloader.XmlDataLoaderTask
 
file - Variable in class org.intermine.objectstore.intermine.TorqueModelOutput
 
file - Variable in class org.intermine.task.FullXmlConverterTask
 
file - Variable in class org.intermine.task.InheritanceDotTask
 
FileConverter - Class in org.intermine.dataconversion
Parent class for DataConverters that read from files
FileConverter(ItemWriter, Model) - Constructor for class org.intermine.dataconversion.FileConverter
Constructor
FileConverterTask - Class in org.intermine.task
Initiates retrieval and conversion of data from a source file.
FileConverterTask() - Constructor for class org.intermine.task.FileConverterTask
 
FileDirectDataLoaderTask - Class in org.intermine.task
A DirectDataLoaderTask for files.
FileDirectDataLoaderTask() - Constructor for class org.intermine.task.FileDirectDataLoaderTask
 
FileDownloadAction - Class in org.intermine.web.struts
This is a generic action to download file from any given directory.
FileDownloadAction() - Constructor for class org.intermine.web.struts.FileDownloadAction
 
FileName - Class in org.intermine.task
 
FileName() - Constructor for class org.intermine.task.FileName
 
fileName - Variable in class org.intermine.web.task.DumpDefaultTemplatesTask
 
fileName - Variable in class org.intermine.web.task.ProfileWriteTask
 
fileName - Variable in class org.intermine.web.task.TemplateTrackWriteTask
 
FILENAME_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
The parameter for setting the filename
fileSet - Variable in class org.intermine.bio.dataconversion.UniprotFilterTask
 
fileSet - Variable in class org.intermine.bio.task.GFF3ConverterTask
 
fileSet - Variable in class org.intermine.dataloader.XmlDataLoaderTask
 
fileSet - Variable in class org.intermine.task.FileConverterTask
 
fileSet - Variable in class org.intermine.task.FullXmlConverterTask
 
fileSets - Variable in class org.intermine.task.FileDirectDataLoaderTask
 
filter(BufferedReader, BufferedWriter) - Method in class org.intermine.bio.dataconversion.UniprotXmlFilter
Filter a UniProt XML dump file, write entries for organisms of interest to a new BufferedWriter.
filter(List<Constraint>, FromElement, boolean) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Return a subset of the given List that contains only Constraints that relate to the given FromElement or constraints associated with nothing if fromElement is null.
filter - Variable in class org.intermine.web.logic.widget.WidgetLdr
 
filter - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
filterByList(Map<String, WebSearchable>, String) - Static method in class org.intermine.web.struts.WebSearchableListController
Filters websearchables.
filterByTags(Map<String, W>, List<String>, String, String, TagManager) - Method in class org.intermine.api.search.SearchFilterEngine
Given a Map from name to WebSearchable, return a Map that contains only those name, WebSearchable pairs where the name is tagged with all of the tags listed.
filterByTags(Map<String, W>, List<String>, String, String, TagManager, boolean) - Method in class org.intermine.api.search.SearchFilterEngine
Given a Map from name to WebSearchable, return a Map that contains only those name, WebSearchable pairs where the name is tagged with all of the tags listed.
filterConfig - Variable in class org.intermine.web.filters.SetCharacterEncodingFilter
The filter configuration object we are associated with.
FilteringResultIterator - Class in org.intermine.webservice.server.output
A result iterator that skips things we aren't interested in.
FilteringResultIterator(Results) - Constructor for class org.intermine.webservice.server.output.FilteringResultIterator
Construct a new iterator which does no filtering.
FilteringResultIterator(Results, int, int, String) - Constructor for class org.intermine.webservice.server.output.FilteringResultIterator
Construct a new iterator which filters to things that match a filter term and only returns results in a given window.
filterOutInvalidTemplates(Map<String, ? extends WebSearchable>) - Static method in class org.intermine.api.search.SearchResults
Filter out invalid templates from a map.
filterWebSearchables(String, String, List<String>, String, String, String) - Static method in class org.intermine.dwr.AjaxServices
Given a scope, type, tags and some filter text, produce a list of matching WebSearchable, in a format useful in JavaScript.
finalize() - Method in class org.intermine.api.tracker.TrackerDelegate
clean up threads
finalize() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Overrides Object.finalize - release the DB log connection.
finalize() - Method in class org.intermine.sql.Database
find(Map<String, Object>) - Method in class org.intermine.webservice.client.lists.ItemList
Convenience method for finding members of a collection matching certain properties.
findAndCodes(Set<String>, LogicExpression.Node) - Static method in class org.intermine.api.query.MainHelper
Finds all the codes in a constraint logic that are ANDed in the given constraint logic.
findClassKeyValue(Map<String, List<FieldDescriptor>>, InterMineObject) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return the first non-null class key field for the object with the given id.
findCombinations(Set<T>, Set<T>, Comparator<? super T>) - Static method in class org.intermine.util.MappingUtil
Produces a Set of possible mappings from items in the firstSet onto items in the secondSet, where the mapping maps from one item to another item that is equal according to the comparator.
findCombinations(Set<T>, Set<T>, Comparator<? super T>, MappingUtilChecker<T>) - Static method in class org.intermine.util.MappingUtil
Produces a Set of possible mappings from items in the firstSet onto items in the secondSet, where the mapping maps from one item to another item that is equal according to the comparator.
findCommonClasses(Collection<ClassDescriptor>) - Static method in class org.intermine.metadata.DescriptorUtils
Return a list of the classes which present in the inheritance tree of all the given classes.
findCommonClasses(Set<ClassDescriptor>) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils
 
findCommonSuperclass(Collection<Class<?>>) - Static method in class org.intermine.util.CollectionUtil
Finds a common superclass or superinterface for all the classes specified in the arguments.
findCommonSuperclasses(Collection<Class<?>>) - Static method in class org.intermine.util.CollectionUtil
Finds common superclasses and superinterfaces for all the classes specified in the arguments.
findCommonSuperTypeOf(Set<ClassDescriptor>) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils
Finds the common class for a set of classes.
findConnectingClasses(ObjectStore, Class<? extends FastPathObject>, String, Class<? extends FastPathObject>, String, Class<? extends FastPathObject>, boolean) - Static method in class org.intermine.bio.postprocess.PostProcessUtil
Return an iterator over the results of a query that connects two classes by a third using arbitrary fields.
findDuplicateSymbols(String) - Method in class org.intermine.bio.dataconversion.NcbiGeneInfoParser
 
findForcedInnerJoins(PathQuery) - Static method in class org.intermine.web.logic.querybuilder.QueryBuilderSummaryHelper
Get a list of paths that should be forced to inner join.
FindInListAction - Class in org.intermine.web.struts
Action to search a list for an identifier and then highlight it on the list details page.
FindInListAction() - Constructor for class org.intermine.web.struts.FindInListAction
 
FindInListForm - Class in org.intermine.web.struts
Form for FindInListAction.
FindInListForm() - Constructor for class org.intermine.web.struts.FindInListForm
Construct a new Form.
findIntersectionType(Collection<ClassDescriptor>) - Static method in class org.intermine.metadata.DescriptorUtils
Find the ClassDescriptor for the type that any two or more objects must be of where those objects are randomly selected from a collection containing objects which are of the types represented by the class descriptors in the provided collection.
findLocationAndObjects(ObjectStore, Class<?>, Class<?>, boolean, boolean, boolean, int) - Static method in class org.intermine.bio.util.BioQueries
Query ObjectStore for all Location object between given object (eg.
findLockedPaths(PathQuery) - Static method in class org.intermine.web.logic.querybuilder.QueryBuilderSummaryHelper
Get a list of paths that should not be removed from the query by the user.
findMostSpecificCommonTypeOf(Set<ClassDescriptor>) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils
 
findMultipleCombinations(Set<Map<T, T>>) - Static method in class org.intermine.util.MappingUtil
Produces a Set of possible combinations of multiple mappings (as produced by findCombinations), where all mappings in a multiple mapping combination map onto distinct objects.
findNewQueryName(Set<String>) - Static method in class org.intermine.api.util.NameUtil
Return a query name that isn't currently in use.
findNewQueryName(Set<String>, String) - Static method in class org.intermine.api.util.NameUtil
Return a query name that isn't currently in use, returning the given name if it is available.
findParentPaths(String, PathQuery) - Static method in class org.intermine.web.logic.querybuilder.QueryBuilderSummaryHelper
Returns a List of paths, being the given path and all its parents.
findParticipatingLoops(LogicExpression, Map<PathConstraint, String>) - Static method in class org.intermine.api.query.MainHelper
Returns the Set of PathConstraintLoop objects that will participate in the QueryClass collapsing mechanism.
findProcessor(Class<? extends ChadoProcessor>) - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
Look at the list of completed processors and return the processor of the given type.
findProteinPathways(ObjectStore) - Static method in class org.intermine.bio.postprocess.ReactomePostProcess
Run a query that returns all proteins, genes, and associated pathways.
findReferencedDescriptor() - Method in class org.intermine.metadata.ReferenceDescriptor
sort out references from this class
findResourcesMatching(Pattern) - Method in class org.intermine.web.struts.ResourceFinder
Find all resources matching a pattern in the WEB-INF directory.
findSumType(Collection<ClassDescriptor>) - Static method in class org.intermine.metadata.DescriptorUtils
Find the ClassDescriptor for the type that any random element selected from a collection of objects must be an instance of, where each object is an instance of one of the classes represented by the class descriptors in the input collection.
findSuperClassNames(Model, String) - Static method in class org.intermine.metadata.ClassDescriptor
Return a list of the super class names for the given class name.
findTableForAlias(String, Set<AbstractTable>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Finds a table in a Set with the given alias.
findTableNames(Query, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Builds a Set of all table names that are touched by a given query.
findTableNames(Query, DatabaseSchema, boolean) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Builds a Set of all table names that are touched by a given query.
finish() - Method in class org.intermine.util.ObjectPipe
Marks the ObjectPipe as finished - that is, no further Objects will be put into the ObjectPipe.
finishedItem(Item) - Method in class org.intermine.xml.full.FullHandler
Method that does something useful with the finished Item
finishedProcessing(Connection, Map<Integer, FeatureData>) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Perform any actions needed after all processing is finished.
finishedProcessing(Connection, Map<Integer, FeatureData>) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Perform any actions needed after all processing is finished.
fireEvent(OriginatingEvent) - Method in class org.intermine.api.profile.StorableBag
 
fireEvent(OriginatingEvent) - Method in interface org.intermine.api.search.WebSearchable
Notify all your observers of this event which originates at this web searchable.
fireEvent(OriginatingEvent) - Method in class org.intermine.api.template.ApiTemplate
 
first() - Method in class org.intermine.webservice.client.results.Page
Get the first page.
firstOrderByHasNoNulls - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
firstPage() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Go to the first page
fixedEnumOps(Class<?>) - Static method in class org.intermine.objectstore.query.SimpleConstraint
For an argument type which an enumerated value set, return the list of operators for which it makes sense only to provide the enumerated values and not allow the user to enter an arbitrary string.
fixEntityNames(String) - Static method in class org.intermine.util.XmlUtil
Replace greek character entity names with entity names that work in HTML.
fixFeatureType(String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Fix types from the feature table, perhaps by changing non-SO type into their SO equivalent.
fixIdentifier(FeatureData, String) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Convert ISO entities from FlyBase to HTML entities.
fixIdentifier(FeatureData, String) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Process the identifier and return a "cleaned" version.
fixIdentifier(FeatureData, String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Process the identifier and return a "cleaned" version.
fixIdentifier(FeatureData, String, String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Process the identifier and return a "cleaned" version.
fixIdentifier(FeatureData, String) - Method in class org.intermine.bio.dataconversion.WormBaseProcessor
Process the identifier and return a "cleaned" version.
fixInvalidBag(String, String) - Method in class org.intermine.api.profile.Profile
Fix this bag by changing its type
fixPubMedId(String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Parser a pubmed id from a results string, extracted to a method so subclasses can override and fix prefixed pubmed ids.
fixPubMedId(String) - Method in class org.intermine.bio.dataconversion.WormBaseProcessor
Wormbase chado has pmid prefixed to pubmed identifiers
fixUpForJoinStyle() - Method in class org.intermine.pathquery.PathQuery
Fixes up the order by list and the constraint logic, given the arrangement of outer joins in the query.
FLAT_FILES - Static variable in enum org.intermine.webservice.server.Format
Flat file formats: TSV, CSV
FlatFileFormatter - Class in org.intermine.webservice.server.output
A class to define behaviour common to flat files (csv, tsv)
FlatFileFormatter() - Constructor for class org.intermine.webservice.server.output.FlatFileFormatter
 
FlatFileWidgetResultProcessor - Class in org.intermine.webservice.server.widget
A widget result processor that produces results in flat file format (tsv/csv)
FlatListFormatter - Class in org.intermine.webservice.server.lists
Formats a list into its name.
FlatListFormatter() - Constructor for class org.intermine.webservice.server.lists.FlatListFormatter
 
flatten(Object) - Static method in class org.intermine.metadata.TypeUtil
Make all nested objects top-level in returned collection
FlatWidgetProcessor - Class in org.intermine.webservice.server.widget
 
FLOOR - Static variable in class org.intermine.objectstore.query.QueryFunction
Greatest integer value less than input.
flush() - Method in class org.intermine.dataloader.DataTracker
Flushes everything to the backing database.
flush() - Method in class org.intermine.sql.logging.DatabaseWriter
Flush completed rows to the database
flush() - Method in class org.intermine.sql.precompute.OptimiserCache
Removes all entries from the cache.
flush(Connection) - Method in class org.intermine.sql.writebatch.Batch
Flushes the batch out to the database server.
flush(Connection, Set<String>) - Method in class org.intermine.sql.writebatch.Batch
Flushes the batch out to the database server.
flush() - Method in interface org.intermine.sql.writebatch.FlushJob
Performs the flush of all data represented by this object.
flush() - Method in class org.intermine.sql.writebatch.FlushJobBatchCommit
Performs the flush of all data represented by this object.
flush() - Method in class org.intermine.sql.writebatch.FlushJobPostgresCopyImpl
Performs the flush of all data represented by this object.
flush() - Method in class org.intermine.sql.writebatch.FlushJobStatementBatchImpl
Performs the flush of all data represented by this object.
flush() - Method in class org.intermine.sql.writebatch.FlushJobUpdateStatistics
Performs the flush of all data represented by this object.
flush() - Method in class org.intermine.webservice.server.output.HTMLOutput
Prints html closing tags.
flush() - Method in class org.intermine.webservice.server.output.MemoryOutput
Does nothing because MemoryOutput serves as a storage of results during execution.
flush() - Method in class org.intermine.webservice.server.output.Output
Flushes output.
flush() - Method in class org.intermine.webservice.server.output.StreamedOutput
Finish writing.
FlushJob - Interface in org.intermine.sql.writebatch
An interface representing a job to be performed when actually flushing data to a database.
FlushJobBatchCommit - Class in org.intermine.sql.writebatch
A FlushJob that commits and re-opens a transaction on the database.
FlushJobBatchCommit(Connection) - Constructor for class org.intermine.sql.writebatch.FlushJobBatchCommit
Constructor for this class
FlushJobPostgresCopyImpl - Class in org.intermine.sql.writebatch
An implementation of the FlushJob interface that represents a batch created in a Statement.
FlushJobPostgresCopyImpl(CopyManager, String, byte[], int) - Constructor for class org.intermine.sql.writebatch.FlushJobPostgresCopyImpl
Constructor for this class
FlushJobStatementBatchImpl - Class in org.intermine.sql.writebatch
An implementation of the FlushJob interface that represents a batch created in a Statement.
FlushJobStatementBatchImpl(Statement) - Constructor for class org.intermine.sql.writebatch.FlushJobStatementBatchImpl
Constructor for this class
FlushJobUpdateStatistics - Class in org.intermine.sql.writebatch
An interface representing a job to be performed when actually flushing data to a database.
FlushJobUpdateStatistics(Map<String, Integer>, BatchWriter, Connection) - Constructor for class org.intermine.sql.writebatch.FlushJobUpdateStatistics
Constructor for this class
flushLogTable() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Allows the log table to be flushed, guaranteeing that all log entries are committed to the database.
flushObjectById() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Completely empties the getObjectById cache.
flushObjectById() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Completely empties the getObjectById cache.
flushObjectById() - Method in interface org.intermine.objectstore.ObjectStore
Completely empties the getObjectById cache.
flushObjectById() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Completely empties the getObjectById cache.
flushObjectById() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Completely empties the getObjectById cache.
flushOldTempBagTables(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Removes any temporary bag tables that are no longer reachable.
FLY_LINK - Static variable in class org.intermine.bio.web.export.GFF3Exporter
for the gff header, link to taxomony
FlyAtlasDisplayer - Class in org.flymine.web.displayer
Displayer for flyatlas expression data.
FlyAtlasDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.flymine.web.displayer.FlyAtlasDisplayer
 
FLYBASE_MISCELLANEOUS_CV - Static variable in class org.intermine.bio.dataconversion.FlyBaseProcessor
The cv.name for the FlyBase miscellaneous CV.
FLYBASE_SO_CV_NAME - Static variable in class org.intermine.bio.dataconversion.FlyBaseProcessor
The cv.name for the FlyBase miscellaneous CV.
FlyBaseCDSFastaLoaderTask - Class in org.intermine.bio.dataconversion
A fasta loader that understand the headers of FlyBase fasta CDS fasta files and can make the appropriate extra objects and references.
FlyBaseCDSFastaLoaderTask() - Constructor for class org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask
 
FlyBaseExpressionDisplayer - Class in org.intermine.bio.web.displayer
FlyBase modENCODE expression data
FlyBaseExpressionDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.FlyBaseExpressionDisplayer
Constructor
FlyBaseFeatureFastaLoaderTask - Class in org.intermine.bio.dataconversion
Code for loading fasta for flybase, setting feature attribute from the FASTA header.
FlyBaseFeatureFastaLoaderTask() - Constructor for class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask
 
FlyBaseIdResolverFactory - Class in org.intermine.bio.dataconversion
Create an IdResolver for Drosophila genes by querying tables in a FlyBase chado database.
FlyBaseIdResolverFactory() - Constructor for class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory
Construct with class name/feature type to read from chado database or file.
FlyBaseIdResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory
Construct with class name/feature type to read from chado database or file.
FlyBaseIdResolverFactory(Set<String>) - Constructor for class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory
Construct with class name/feature type to read from chado database or file.
FlyBasePostProcess - Class in org.intermine.bio.postprocess
Copy transcript.introns to gene.introns.
FlyBasePostProcess(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.FlyBasePostProcess
Create a new instance of FlyBasePostProcess
FlyBaseProcessor - Class in org.intermine.bio.dataconversion
A converter for chado that handles FlyBase specific configuration.
FlyBaseProcessor(ChadoDBConverter) - Constructor for class org.intermine.bio.dataconversion.FlyBaseProcessor
Create a new FlyBaseChadoDBConverter.
FlyBaseUniProtRefsTask - Class in org.intermine.bio.postprocess
Task to read a file mapping cds identifiers to UniProt accession numbers and create a protein reference in the CDSs.
FlyBaseUniProtRefsTask() - Constructor for class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask
 
FlyBaseUTRFastaLoaderTask - Class in org.intermine.bio.dataconversion
A fasta loader that understand the headers of FlyBase fasta UTR fasta files and can make the appropriate extra objects and references.
FlyBaseUTRFastaLoaderTask() - Constructor for class org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask
 
followProjectDependencies(String, List, List<String>) - Method in class org.intermine.task.Dependencies
Load dependencies for a project and iterate over them.
format(String) - Static method in class org.intermine.pathquery.ConstraintValueParser
Converts a Date to ISO date format.
format(List<? extends Object>) - Method in interface org.intermine.web.logic.export.RowFormatter
Format row to string.
format(List<? extends Object>) - Method in class org.intermine.web.logic.export.RowFormatterImpl
Formats objects to string.
format(double, StringBuffer, FieldPosition) - Method in class org.intermine.web.logic.widget.GraphWidget.DivNumberFormat
 
format(long, StringBuffer, FieldPosition) - Method in class org.intermine.web.logic.widget.GraphWidget.DivNumberFormat
 
Format - Enum in org.intermine.webservice.server
 
format(Job) - Method in class org.intermine.webservice.server.idresolution.BagResultCategoryKeyFormatter
 
format(Job) - Method in interface org.intermine.webservice.server.idresolution.BagResultFormatter
Turn a job into a serialisable structure.
format(Job) - Method in class org.intermine.webservice.server.idresolution.BagResultOutputKeyFormatter
 
format(InterMineBag) - Method in class org.intermine.webservice.server.lists.FlatListFormatter
 
format(InterMineBag) - Method in class org.intermine.webservice.server.lists.HtmlListFormatter
 
format(InterMineBag) - Method in class org.intermine.webservice.server.lists.JSONListFormatter
 
format(InterMineBag) - Method in interface org.intermine.webservice.server.lists.ListFormatter
Format a list into a list of string values.
format(PermanentToken) - Static method in class org.intermine.webservice.server.user.PermaTokens
Format a permanent token as a map.
FORMAT_PARAMETER_ANY - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
The parameter for accepting any format
FORMAT_PARAMETER_COUNT - Static variable in class org.intermine.webservice.client.core.RequestImpl
 
FORMAT_PARAMETER_COUNT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants comma separated output to be returned.
FORMAT_PARAMETER_CSV - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants comma separated output to be returned.
FORMAT_PARAMETER_HTML - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants html output to be returned.
FORMAT_PARAMETER_JSON - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data
FORMAT_PARAMETER_JSON_COUNT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data suitable for using to construct tables with - this returns the rows of the table
FORMAT_PARAMETER_JSON_DATA_TABLE - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data in a data table
FORMAT_PARAMETER_JSON_OBJ - Static variable in class org.intermine.webservice.client.core.RequestImpl
 
FORMAT_PARAMETER_JSON_OBJ - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data as nested objects representing records
FORMAT_PARAMETER_JSON_ROW - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data suitable for using to construct tables with - this returns the rows of the table
FORMAT_PARAMETER_JSON_ROWS - Static variable in class org.intermine.webservice.client.core.RequestImpl
 
FORMAT_PARAMETER_JSON_TABLE - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data suitable for using to construct tables with
FORMAT_PARAMETER_JSONP - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants jsonp data
FORMAT_PARAMETER_JSONP_COUNT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data as above but in a format suitable for cross site ajax calls
FORMAT_PARAMETER_JSONP_DATA_TABLE - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants jsonp data in a data table
FORMAT_PARAMETER_JSONP_OBJ - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data as above, but in a format suitable for cross site ajax calls
FORMAT_PARAMETER_JSONP_ROW - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data as above but in a format suitable for cross site ajax calls
FORMAT_PARAMETER_JSONP_TABLE - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data as above but in a format suitable for cross site ajax calls
FORMAT_PARAMETER_TAB - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants tab separated output to be returned.
FORMAT_PARAMETER_TEXT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants plain text to be returned.
FORMAT_PARAMETER_TSV - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants tab separated output to be returned.
FORMAT_PARAMETER_XML - Static variable in class org.intermine.webservice.client.core.RequestImpl
 
FORMAT_PARAMETER_XML - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants xml output to be returned.
FORMAT_VERSION - Static variable in class org.intermine.objectstore.intermine.TorqueModelOutput
The version number of the database format
formatAttributes(Map<String, Object>, StringBuilder) - Method in class org.intermine.webservice.server.output.JSONFormatter
Format the header attributes.
formatAttributes(Map<String, Object>, StringBuilder) - Method in class org.intermine.webservice.server.output.JSONResultFormatter
This differs from the JSONFormatter implementation in that it will output a representation of all keys in the attributes map.
formatClass(ClassDescriptor, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Formats a class name, using the web-config to produce configured labels.
formatColumnName(String) - Static method in class org.intermine.web.logic.WebUtil
Formats column name.
formatExtraAttributes(Map<String, Map<String, Object>>) - Method in class org.intermine.webservice.server.widget.EnrichmentJSONProcessor
Format the value of extraAttribute.
formatField(String, InterMineAPI, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Format a path into a displayable field name.
formatField(Path, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Format a path into a displayable field name.
formatFieldChain(Path, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Format a sequence of fields in a chain.
formatFieldChain(String, InterMineAPI, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Format a path represented as a string to the formatted fields, without the class name.
formatFooter(String, int) - Method in class org.intermine.webservice.server.jbrowse.util.ArrayFormatter
 
formatFooter(String, int) - Method in class org.intermine.webservice.server.jbrowse.util.ObjectFormatter
 
formatFooter(String, int) - Method in class org.intermine.webservice.server.output.FlatFileFormatter
 
formatFooter(String, int) - Method in class org.intermine.webservice.server.output.Formatter
Returns formatted footer.
formatFooter(String, int) - Method in class org.intermine.webservice.server.output.JSONFormatter
Put on the final brace, and close the call-back bracket if needed.
formatFooter(String, int) - Method in class org.intermine.webservice.server.output.PlainFormatter
 
formatFooter(String, int) - Method in class org.intermine.webservice.server.output.XMLFormatter
 
formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.jbrowse.util.ArrayFormatter
 
formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.jbrowse.util.ObjectFormatter
 
formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.output.FlatFileFormatter
Returns formatted header.
formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.output.Formatter
Returns formatted header.
formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONFormatter
Add the opening brace, and a call-back if any
formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.output.PlainFormatter
 
formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.output.XMLFormatter
 
formatIsFlatFile() - Method in class org.intermine.webservice.server.WebService
 
formatIsJSON() - Method in class org.intermine.webservice.server.WebService
 
formatIsJsonObj() - Method in class org.intermine.webservice.server.query.AbstractQueryService
 
formatIsJSONP() - Method in class org.intermine.webservice.server.WebService
 
formatIsXML() - Method in class org.intermine.webservice.server.WebService
 
formatKVPair(String, Object) - Method in class org.intermine.pathquery.PathQuery
Format a key-value pair in a JSON compatible way.
formatPath(String, HttpServletRequest) - Static method in class org.intermine.web.logic.WebUtil
Formats a column name, using the webconfig to produce configured labels.
formatPath(String, Model, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Formats a column name, using the webconfig to produce configured labels.
formatPath(String, InterMineAPI, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Formats a column name, using the webconfig to produce configured labels.
formatPath(String, PathQuery, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Formats a column name, using the given query to construct a path according to the current state of its subclasses.
formatPath(Path, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Formats a column name, using the webconfig to produce configured labels.
formatPathDescription(String, PathQuery, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Return a string suitable for displaying a PathQuery's path, taking any path descriptions it has configured into account.
formatPathDescription(Path, PathQuery, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Return a string suitable for displaying a PathQuery's path, taking any path descriptions it has configured into account.
formatPathQueryView(PathQuery, HttpServletRequest) - Static method in class org.intermine.web.logic.WebUtil
Format a query's view into a list of displayable strings, taking both the query's path descriptions and the application's web configuration into account.
formatPathQueryView(PathQuery, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Format a query's view into a list of displayable strings, taking both the query's path descriptions and the application's web configuration into account.
formatResult(List<String>) - Method in class org.intermine.webservice.server.jbrowse.util.ArrayFormatter
 
formatResult(List<String>) - Method in class org.intermine.webservice.server.output.FlatFileFormatter
 
formatResult(List<String>) - Method in class org.intermine.webservice.server.output.Formatter
Returns formatted result item.
formatResult(List<String>) - Method in class org.intermine.webservice.server.output.JSONCountFormatter
 
formatResult(List<String>) - Method in class org.intermine.webservice.server.output.JSONFormatter
In normal cases a list with a single JSON string item is expected.
formatResult(List<String>) - Method in class org.intermine.webservice.server.output.PlainFormatter
 
formatResult(List<String>) - Method in class org.intermine.webservice.server.output.XMLFormatter
Returns formatted result item.
formatResult(KeywordSearchResult, boolean) - Method in class org.intermine.webservice.server.search.QuickSearchJSONProcessor
 
formatResult(KeywordSearchResult, boolean) - Method in interface org.intermine.webservice.server.search.QuickSearchResultProcessor
They take a results, and return one or more strings.
formatResult(KeywordSearchResult, boolean) - Method in class org.intermine.webservice.server.search.QuickSearchTextProcessor
 
formatResult(KeywordSearchResult, boolean) - Method in class org.intermine.webservice.server.search.QuickSearchXMLProcessor
 
formatResult(List<String>) - Method in class org.intermine.webservice.server.user.UserDataFormatter
 
formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.EnrichmentJSONProcessor
 
formatRow(List<Object>) - Method in interface org.intermine.webservice.server.widget.EnrichmentResultProcessor
Format a row of results.
formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.EnrichmentXMLProcessor
 
formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.FlatFileWidgetResultProcessor
 
formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.GraphJSONProcessor
 
formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.GraphXMLProcessor
 
formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.TableJSONProcessor
 
formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.TableXMLProcessor
 
formatRow(List<Object>) - Method in interface org.intermine.webservice.server.widget.WidgetResultProcessor
Format a list of objects into a string representation.
FormattedTextParser - Class in org.intermine.util
Class for methods and util methods for parsing csv files and others.
Formatter - Class in org.intermine.webservice.server.output
Abstract class for formatting result data.
Formatter() - Constructor for class org.intermine.webservice.server.output.Formatter
 
formFile - Variable in class org.intermine.web.struts.ImportXMLForm
 
ForseenProblem - Exception in org.intermine.web.struts.oauth2
An exception type to plaster over the absence of first-class continuations in java.
ForseenProblem(String) - Constructor for exception org.intermine.web.struts.oauth2.ForseenProblem
Construct one of these objects.
ForseenProblem(String, Object...) - Constructor for exception org.intermine.web.struts.oauth2.ForseenProblem
Construct one of these objects.
forward() - Method in class org.intermine.web.struts.ForwardParameters
Construct the resulting ActionForward.
ForwardParameters - Class in org.intermine.web.struts
Utility wrapper class for programatically adding parameters to ActionForward paths.
ForwardParameters(ActionForward) - Constructor for class org.intermine.web.struts.ForwardParameters
Creates a new instance of ForwardParameters.
ForwardParameters(String, boolean) - Constructor for class org.intermine.web.struts.ForwardParameters
Creates a new instance of ForwardParameters with a given path and redirect settings.
FriendlyMineLinkController - Class in org.intermine.bio.web
Gets list of friendly intermines to show on list analysis page.
FriendlyMineLinkController() - Constructor for class org.intermine.bio.web.FriendlyMineLinkController
 
FriendlyMineLinkGenerator - Class in org.intermine.bio.web.displayer
Helper class for intermine links generated on report and lists pages
FriendlyMineLinkGenerator() - Constructor for class org.intermine.bio.web.displayer.FriendlyMineLinkGenerator
Constructor
friendlyMineManager - Variable in class org.intermine.api.InterMineAPI
 
FriendlyMineManager - Class in org.intermine.api.mines
Class to manage friendly mines
from - Variable in class org.intermine.sql.query.Query
 
FROM_DB - Static variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
FromElement - Interface in org.intermine.objectstore.query
An element that can appear in the FROM clause of a query
full - Variable in class org.intermine.sql.precompute.BestQueryLogger
 
full - Variable in class org.intermine.task.AnalyseDbTask
 
FullHandler - Class in org.intermine.xml.full
Extension of DefaultHandler to handle parsing full XML.
FullHandler() - Constructor for class org.intermine.xml.full.FullHandler
Create a new FullHandler object.
FullParser - Class in org.intermine.xml.full
Unmarshal XML Full format data into java business objects.
FullRenderer - Class in org.intermine.xml.full
Render an object in InterMine Full XML format
FullTimeLdr - Class in org.intermine.model.testmodel.web.widget
 
FullTimeLdr(InterMineBag, ObjectStore, String) - Constructor for class org.intermine.model.testmodel.web.widget.FullTimeLdr
 
FullXmlConverter - Class in org.intermine.dataconversion
Loads InterMine XML into an items database.
FullXmlConverter(ItemWriter, Model) - Constructor for class org.intermine.dataconversion.FullXmlConverter
Constructor.
FullXmlConverterTask - Class in org.intermine.task
Load InterMine Items XML file(s) into a target items database.
FullXmlConverterTask() - Constructor for class org.intermine.task.FullXmlConverterTask
 
Function - Class in org.intermine.sql.query
A representation of a function in an SQL query.
Function(int) - Constructor for class org.intermine.sql.query.Function
Constructor for this Function object.
Function<A,B> - Interface in org.intermine.webservice.server.core
An interface for defining a thing that can take something and return something else.

G

GAFExporter - Class in org.intermine.bio.web.export
Exports LocatedSequenceFeature objects to GO Annotation File Format 2.0
GAFExporter(PrintWriter, List<Integer>, Collection<String>) - Constructor for class org.intermine.bio.web.export.GAFExporter
Constructor.
GAFQueryService - Class in org.intermine.bio.webservice
A service for exporting query results in GAF format.
GAFQueryService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.GAFQueryService
Constructor.
GAFQueryServlet - Class in org.intermine.bio.webservice
A servlet to hand off to the GAF query service.
GAFQueryServlet() - Constructor for class org.intermine.bio.webservice.GAFQueryServlet
 
GAFRecord - Class in org.intermine.bio.io.gaf
A record in a BED formatted file.
GAFRecord(String, int, int, String, int, String) - Constructor for class org.intermine.bio.io.gaf.GAFRecord
Constructor The following five attributes are normally hosted in InterMine cases.
GAFUtil - Class in org.intermine.bio.web.export
Utility methods for GAF format.
GalaxyExportAction - Class in org.intermine.bio.web.struts
Generate feature path query.
GalaxyExportAction() - Constructor for class org.intermine.bio.web.struts.GalaxyExportAction
 
GalaxyExportForm - Class in org.intermine.bio.web.struts
 
GalaxyExportForm() - Constructor for class org.intermine.bio.web.struts.GalaxyExportForm
 
GalaxyExportOptionsController - Class in org.intermine.bio.web.struts
Controller for galaxyExportOptions.tile.
GalaxyExportOptionsController() - Constructor for class org.intermine.bio.web.struts.GalaxyExportOptionsController
 
GBrowseDisplayer - Class in org.intermine.bio.web.displayer
Displayer for GBrowse
GBrowseDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.GBrowseDisplayer
Construct with config and the InterMineAPI.
gcd(int, int) - Static method in class org.intermine.metadata.Util
Takes two integers, and returns the greatest common divisor, using euclid's algorithm.
GeneExpressionAtlasDiseasesDisplayer - Class in org.intermine.bio.web.displayer
Gene Expression Atlas Displayer (Blue/Green)
GeneExpressionAtlasDiseasesDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.GeneExpressionAtlasDiseasesDisplayer
Constructor
GeneExpressionAtlasDiseasesExpressions - Class in org.intermine.bio.web.model
Gene Expression Atlas Tissues Expressions
GeneExpressionAtlasDiseasesExpressions(ExportResultsIterator) - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions
Convert Path results into a List (ProteinAtlasDisplayer.java)
GeneExpressionAtlasDiseasesExpressions.ByPValueComparator - Class in org.intermine.bio.web.model
Sort by p-value inversely
GeneExpressionAtlasDiseasesExpressions.ByPValueComparator() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ByPValueComparator
 
GeneExpressionAtlasDiseasesExpressions.ByTStatisticComparator - Class in org.intermine.bio.web.model
Sort by t-statistic
GeneExpressionAtlasDiseasesExpressions.ByTStatisticComparator() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ByTStatisticComparator
 
GeneExpressionAtlasDiseasesExpressions.CaseInsensitiveComparator - Class in org.intermine.bio.web.model
Comparator used on "conditions" to sort them (their keys) case insensitively
GeneExpressionAtlasDiseasesExpressions.CaseInsensitiveComparator() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.CaseInsensitiveComparator
 
GeneExpressionAtlasDiseasesExpressions.ExpressionList - Class in org.intermine.bio.web.model
Represents a list of expressions (taken from multiple probe sets) for a given tissue type
GeneExpressionAtlasDiseasesExpressions.ExpressionList() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ExpressionList
Constructor
GeneExpressionAtlasTissuesDisplayer - Class in org.intermine.bio.web.displayer
Gene Expression Atlas Displayer (Blue/Green)
GeneExpressionAtlasTissuesDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.GeneExpressionAtlasTissuesDisplayer
Constructor
GeneExpressionAtlasTissuesExpressions - Class in org.intermine.bio.web.model
Gene Expression Atlas Tissues Expressions
GeneExpressionAtlasTissuesExpressions(ExportResultsIterator) - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions
Convert Path results into a List (ProteinAtlasDisplayer.java)
GeneExpressionAtlasTissuesExpressions.ByPValueComparator - Class in org.intermine.bio.web.model
Sort by p-value inversely
GeneExpressionAtlasTissuesExpressions.ByPValueComparator() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ByPValueComparator
 
GeneExpressionAtlasTissuesExpressions.ByTStatisticComparator - Class in org.intermine.bio.web.model
Sort by t-statistic
GeneExpressionAtlasTissuesExpressions.ByTStatisticComparator() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ByTStatisticComparator
 
GeneExpressionAtlasTissuesExpressions.CaseInsensitiveComparator - Class in org.intermine.bio.web.model
Comparator used on "conditions" to sort them (their keys) case insensitively
GeneExpressionAtlasTissuesExpressions.CaseInsensitiveComparator() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.CaseInsensitiveComparator
 
GeneExpressionAtlasTissuesExpressions.ExpressionList - Class in org.intermine.bio.web.model
Represents a list of expressions (taken from multiple probe sets) for a given tissue type
GeneExpressionAtlasTissuesExpressions.ExpressionList() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ExpressionList
Constructor
geneFile - Variable in class org.intermine.bio.dataconversion.TreefamConverter
 
GeneIdentifiersDisplayer - Class in org.intermine.bio.web.displayer
 
GeneIdentifiersDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.GeneIdentifiersDisplayer
Construct with config and the InterMineAPI.
GeneInfoRecord - Class in org.intermine.bio.dataconversion
Data structure to hold information from one row of an NCBI Entrez gene_info file.
GeneInfoRecord(String, String, String, String, String, String, String, String, String) - Constructor for class org.intermine.bio.dataconversion.GeneInfoRecord
Construct information from file for one gene.
GeneLengthCorrectionCoefficient - Class in org.intermine.bio.web.widget
Implementation of the gene length coefficient
GeneLengthCorrectionCoefficient(WidgetConfig, ObjectStore, InterMineBag) - Constructor for class org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient
 
GeneMicroArrayDisplayerController - Class in org.flymine.web
Controller for geneMicroArrayDisplayer.jsp
GeneMicroArrayDisplayerController() - Constructor for class org.flymine.web.GeneMicroArrayDisplayerController
 
GeneModel - Class in org.intermine.bio.web.model
Representation of a gene model - being one transcript of a gene and including exons, introns, UTRs and CDSs where data are available.
GeneModel(Model, Gene, InterMineObject) - Constructor for class org.intermine.bio.web.model.GeneModel
Construct a new gene model for the given transcript and gene.
GeneModelCache - Class in org.intermine.bio.web.model
A cache for gene models by Gene object id.
GeneModelSettings - Class in org.intermine.bio.web.model
 
GeneModelSettings(String) - Constructor for class org.intermine.bio.web.model.GeneModelSettings
 
GeneOntologyDisplayer - Class in org.intermine.bio.web.displayer
Builds datastructure from go parent id to go term id.
GeneOntologyDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.GeneOntologyDisplayer
Construct with config and the InterMineAPI.
generate(WebserviceCodeGenInfo) - Method in interface org.intermine.api.query.codegen.WebserviceCodeGenerator
This method will generate web service source code from a path query or template query.
generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
This method will generate web service source code in Java from a path query or template query.
generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebserviceJavaScriptCodeGenerator
This method will generate code that can be run in a browser.
generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
This method will generate web service source code in Perl from a path query or template query.
generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
This method will generate code that will run using the python webservice client library.
generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
generate(ClassDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
Generate the output for a ClassDescriptor.
generate(AttributeDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
Generates code for a single attribute.
generate(ReferenceDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
Generates code for a single reference.
generate(CollectionDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
Generates code for a single collection.
generate(Query, int, int, DatabaseSchema, Database, Map<Object, String>) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a Query object into an SQL String.
generate(Query, DatabaseSchema, Database, Constraint, int, Map<Object, String>) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a Query object into an SQL String.
generate() - Method in class org.intermine.objectstore.intermine.TorqueModelOutput
Generate a string that contains the torque data for the given schema.
generate(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.TorqueModelOutput
Generate a string that describes the given ClassDescriptor.
generate24hrKey(Profile) - Method in class org.intermine.api.profile.ProfileManager
Generate a day token
generateAddCollectionElement(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generates the addCollectionElement method.
generateApiKey(Profile) - Method in class org.intermine.api.profile.ProfileManager
Generate a new API access key for this profile and return it.
generateApiKey(String) - Method in class org.intermine.dwr.AjaxServices
Generate a new API key for a given user.
generateCertificate(String, PublicKey) - Method in class org.intermine.web.security.KeySigner
Create a self-signed X.509 Certificate Should be eventually replaced with X509v3CertificateBuilder.
generateClassDescriptors(Reader, String) - Method in class org.intermine.metadata.InterMineModelParser
Read source model information in InterMine XML format and create a set of ClassDescriptors.
generateClassDescriptors(Reader, String) - Method in interface org.intermine.metadata.ModelParser
Read source information and construct a list of InterMine ClassDescriptors
generateClassName(String, String) - Static method in class org.intermine.metadata.TypeUtil
Generate the full class name, eg. org.intermine.bio.SequenceFeature from a SO term and a package name.
generateClassNames(String, Model) - Static method in class org.intermine.xml.full.ItemHelper
Generate a package qualified class name within the specified model from a space separated list of namespace qualified names
generateCreateListHtml(Map<GenomicRegion, List<List<String>>>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Generate a html string with all feature type for list creation.
generateEquals(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generate a .equals() method for the given class.
generateFieldDescriptors(ClassDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
Generate all FieldDescriptors for a class/interface
generateGenomicRegions(Collection<String>) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchUtil
Generate a GenomicRegion object from region strings and relevant information
generateGetElementType(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generates the getElementType method.
generateGetFieldType(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generates the getFieldType method.
generateGetFieldValue(ClassDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
Generates the getFieldValue method.
generateGetObject(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generates the getoBJECT method for producing NotXml.
generateGetSet(FieldDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
Write code for getters and setters for given field.
generateHashCode(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generate a .hashCode() method for the given class.
generateIndirectionTable(CollectionDescriptor) - Method in class org.intermine.objectstore.intermine.TorqueModelOutput
Generate an indirection table
generateJBrowseURL(GenomicRegion, List<String>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Generated a jbrowse url
generateJBrowseURL(GenomicRegion) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
A wrapper of generateJBrowseURL(GenomicRegion s, List featureTypes)
generateJdbcType(String) - Static method in class org.intermine.objectstore.intermine.TorqueModelOutput
Convert java primitive and object names to those compatible with torque.
generateLink(InterMineAPI, InterMineObject) - Method in class org.intermine.api.LinkRedirectManager
 
generateLink(InterMineAPI, InterMineObject) - Method in class org.intermine.bio.web.BioLinkRedirectManager
 
generateLink(InterMineAPI, InterMineObject) - Method in class org.intermine.model.testmodel.web.RedirectManager
 
generateListFromQuery(PathQuery, String, String, Collection<String>, Profile) - Method in class org.intermine.webservice.server.query.QueryListAppendService
 
generateListFromQuery(PathQuery, String, String, Collection<String>, Profile) - Method in class org.intermine.webservice.server.query.QueryToListService
Generate a list from a pathquery.
generateListFromQuery(PathQuery, String, String, Collection<String>, Profile) - Method in class org.intermine.webservice.server.template.TemplateListAppendService
 
generateNewName(Set<String>, String) - Static method in class org.intermine.api.util.NameUtil
Generate a new name for a list.
generatePassword() - Static method in class org.intermine.web.task.LoadDefaultTemplatesTask
Generate a random 8-letter String of lower-case characters
generatePermaLink(FastPathObject, String, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.web.logic.PortalHelper
Generate a perma-link to a report page for an InterMine object.
generatePermaPath(FastPathObject, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.web.logic.PortalHelper
Generate a link suitable for use as an external, permanent link, in that the link should work between rebuilds of the database.
generatePortalLink(FastPathObject, InterMineAPI, HttpServletRequest) - Static method in class org.intermine.web.logic.PortalHelper
Generate a stable link to a report page for the given object, this will create a portal link with the correct class and a value from a non-null class key field of the object.
generatePortalPath(FastPathObject, InterMineAPI) - Static method in class org.intermine.web.logic.PortalHelper
Generate an external portal link (perma-link) for an InterMine object.
generateQueryForId(Integer, Class<?>, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Generates a query to retrieve a single object from the database, by id.
generateRandomUniqueString() - Static method in class org.intermine.api.util.TextUtil
 
generateRandomUniqueString(int) - Static method in class org.intermine.api.util.TextUtil
 
generateReadOnlyAccessToken(Profile, String) - Method in class org.intermine.api.profile.ProfileManager
Return a permanent user access token, with ReadOnly permission.
generateReportLink(ResultElement, String) - Static method in class org.intermine.web.logic.PortalHelper
Generate a link to the object details page using the internal id.
generateReportPath(ResultCell) - Static method in class org.intermine.web.logic.PortalHelper
Get the path fragment (starting with "/") for the report page for an object in the mine.
generateSetFieldValue(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generates the setFieldValue method.
generateSetObject(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generates the setoBJECT method for deserialising objects.
generateSingleUseKey(Profile) - Method in class org.intermine.api.profile.ProfileManager
Generate a single use API key and store it in memory, before returning it.
generateSql(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Generate sql from a Query
generateSql(Connection, Query, int, int) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Create temporary tables for the bag in the BagConstraints of the given Query, then call SqlGenerator.generate().
generateSql(Connection, Query, int, int) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Create temporary tables for the bag in the BagConstraints of the given Query, then call SqlGenerator.generate().
generateSqlCompatibleName(String) - Static method in class org.intermine.sql.DatabaseUtil
Convert any sql keywords to valid names for tables/columns.
generateToString(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generate a .toString() method for the given class .
generationSqlString - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
geneRefId - Variable in class org.intermine.bio.dataconversion.HomologeneConverter.GeneRecord
 
GeneStructureDisplayer - Class in org.intermine.bio.web.displayer
Custom displayer for gene structure.
GeneStructureDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.GeneStructureDisplayer
Construct with config and the InterMineAPI.
geneType - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord
 
GenomeDBConverter - Class in org.intermine.bio.dataconversion
A ChadoDBConverter that sets the dataset and datasource for genome databases (eg.
GenomeDBConverter(Database, Model, ItemWriter) - Constructor for class org.intermine.bio.dataconversion.GenomeDBConverter
Create a new ChadoDBConverter object.
GenomicRegion - Class in org.intermine.bio.web.model
This Java bean represents one record of Chromosome coordinates from user input The record should be in BED format: "chr\tstart\tend".
GenomicRegion() - Constructor for class org.intermine.bio.web.model.GenomicRegion
Default constructor a new GenomicRegion must use setters to set start, end, extendedRegionSize
GenomicRegionBedService - Class in org.intermine.bio.webservice
 
GenomicRegionBedService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.GenomicRegionBedService
Constructor.
GenomicRegionBedServlet - Class in org.intermine.bio.webservice
 
GenomicRegionBedServlet() - Constructor for class org.intermine.bio.webservice.GenomicRegionBedServlet
 
GenomicRegionFastaService - Class in org.intermine.bio.webservice
A class for exposing the region search as a FASTA resource.
GenomicRegionFastaService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.GenomicRegionFastaService
Constructor.
GenomicRegionFastaServlet - Class in org.intermine.bio.webservice
 
GenomicRegionFastaServlet() - Constructor for class org.intermine.bio.webservice.GenomicRegionFastaServlet
 
GenomicRegionGFF3Service - Class in org.intermine.bio.webservice
 
GenomicRegionGFF3Service(InterMineAPI) - Constructor for class org.intermine.bio.webservice.GenomicRegionGFF3Service
Constructor.
GenomicRegionGFF3Servlet - Class in org.intermine.bio.webservice
 
GenomicRegionGFF3Servlet() - Constructor for class org.intermine.bio.webservice.GenomicRegionGFF3Servlet
 
GenomicRegionSearchAction - Class in org.intermine.bio.web.struts
For genomic region search.
GenomicRegionSearchAction() - Constructor for class org.intermine.bio.web.struts.GenomicRegionSearchAction
 
GenomicRegionSearchAjaxAction - Class in org.intermine.bio.web.struts
Genomic region search ajax calls.
GenomicRegionSearchAjaxAction() - Constructor for class org.intermine.bio.web.struts.GenomicRegionSearchAjaxAction
 
GenomicRegionSearchConstraint - Class in org.intermine.bio.web.model
A class to represent the constraints a user selected including a list of features and genomic regions, etc.
GenomicRegionSearchConstraint() - Constructor for class org.intermine.bio.web.model.GenomicRegionSearchConstraint
 
GenomicRegionSearchForm - Class in org.intermine.bio.web.struts
This ActionForm represents the form elements on the genomicRegionSearchOptionsBase.jsp
GenomicRegionSearchForm() - Constructor for class org.intermine.bio.web.struts.GenomicRegionSearchForm
 
GenomicRegionSearchListInput - Class in org.intermine.bio.webservice
 
GenomicRegionSearchListInput(HttpServletRequest, BagManager, Profile, InterMineAPI) - Constructor for class org.intermine.bio.webservice.GenomicRegionSearchListInput
A representation of a request to a region based web service.
GenomicRegionSearchListInput.GenomicRegionSearchInfo - Class in org.intermine.bio.webservice
 
GenomicRegionSearchListInput.GenomicRegionSearchInfo() - Constructor for class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
 
GenomicRegionSearchOptionsController - Class in org.intermine.bio.web.struts
Class to prepare data for genomicRegionSeachOptions.jsp.
GenomicRegionSearchOptionsController() - Constructor for class org.intermine.bio.web.struts.GenomicRegionSearchOptionsController
 
GenomicRegionSearchQueryRunner - Class in org.intermine.bio.web.logic
This class has all database query logics for genomic region search.
GenomicRegionSearchQueryRunner(HttpServletRequest, String, GenomicRegionSearchConstraint, Map<GenomicRegion, Query>) - Constructor for class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner
Constructor
GenomicRegionSearchService - Class in org.intermine.bio.web.logic
A class to provide genomic region search services in general.
GenomicRegionSearchService() - Constructor for class org.intermine.bio.web.logic.GenomicRegionSearchService
Constructor
GenomicRegionSearchService - Class in org.intermine.bio.webservice
A web service resource to expose the Region Search functionality.
GenomicRegionSearchService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.GenomicRegionSearchService
Constructor.
GenomicRegionSearchServlet - Class in org.intermine.bio.webservice
 
GenomicRegionSearchServlet() - Constructor for class org.intermine.bio.webservice.GenomicRegionSearchServlet
 
GenomicRegionSearchUtil - Class in org.intermine.bio.web.logic
This utility class instance a GenomicRegionSearchService object based on mine's setting.
GenomicRegionSequenceExporter - Class in org.intermine.bio.web.export
Exports DNA sequences of given genomic regions in FASTA format.
GenomicRegionSequenceExporter(ObjectStore, OutputStream) - Constructor for class org.intermine.bio.web.export.GenomicRegionSequenceExporter
Instructor
get(int) - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
get(int) - Method in class org.intermine.api.results.WebResults
get(int) - Method in class org.intermine.objectstore.query.Results
get(Object) - Method in class org.intermine.util.AlwaysMap
get(Object) - Method in class org.intermine.util.IdentityMap
get(int) - Method in class org.intermine.util.IntToIntMap
Retrieves a mapping from the object
get(Integer) - Method in class org.intermine.util.IntToIntMap
Retrieves a mapping from the object.
get(Object) - Method in class org.intermine.util.ReferenceMap
get(Path, Profile, PathQuery) - Method in class org.intermine.web.logic.query.DisplayConstraintFactory
Get a display constraint.
get(PathConstraint, Profile, PathQuery) - Method in class org.intermine.web.logic.query.DisplayConstraintFactory
Get a display constraint.
get(Object) - Method in class org.intermine.web.logic.results.ReportObjectFactory
Get a ReportObject for the given InterMineObject.
get(String) - Method in class org.intermine.web.security.KeyStorePublicKeySource
 
get(String) - Method in interface org.intermine.web.security.PublicKeySource
Get a specific key by name.
get(int) - Method in class org.intermine.webservice.client.lists.ItemList
Get an item by its index.
get(int) - Method in class org.intermine.webservice.client.results.JsonRow
 
get(Object) - Method in class org.intermine.webservice.client.results.JsonRowMap
 
get(int) - Method in class org.intermine.webservice.client.results.ResultRowList
 
get(Object) - Method in class org.intermine.webservice.client.results.ResultRowMap
 
getAbbreviation() - Method in class org.intermine.bio.util.OrganismData
Get the abbreviation of this organism.
getAbbreviation(String) - Static method in class org.intermine.webservice.server.CodeTranslator
Returns corresponding abbreviation of translated operation.
getAcceptableFormats(HttpServletRequest) - Static method in class org.intermine.webservice.server.WebServiceRequestParser
Get the list of formats that this request finds acceptable.
getAccepted() - Method in class org.intermine.api.bag.SharingInvite
 
getAccepted() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
getAcceptedAt() - Method in class org.intermine.api.bag.SharingInvite
 
getAcceptedAt() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
getAccessCounter(Connection) - Method in class org.intermine.api.tracker.TemplateTracker
Return the number of executions for each public template
getAccessCounter() - Method in class org.intermine.api.tracker.TrackerDelegate
Return the rank associated to the templates
getAccessibleLists() - Method in class org.intermine.webservice.client.services.ListService
Returns all the lists that this service has access to.
getAccessions() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getAction() - Method in class org.intermine.api.search.TaggingEvent
 
getAction() - Method in class org.intermine.web.struts.WidgetForm
 
getAction() - Method in class org.intermine.webservice.server.jbrowse.Command
 
getActionMessage(String, int, String, String) - Method in class org.intermine.bio.web.logic.OrthologueConverter
Get the ActionMessage to display in the webapp
getActionMessage(String, int, String, String) - Method in class org.intermine.web.logic.bag.BagConverter
Get the ActionMessage to display in the webapp
getActionMessage() - Method in exception org.intermine.web.struts.oauth2.ForseenProblem
Get a struts action message, rather than a simple string message.
getActionType() - Method in class org.intermine.web.struts.TemplateSettingsForm
 
getAdder() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the adder Method.
getAdder(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the Method object that is the adder for the field name
getAddIssues() - Method in class org.intermine.webservice.server.lists.ListCreationInput
 
getAdditionalBeanInfo() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getAdditionalBeanInfo() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getAdditionalConverters(String) - Method in class org.intermine.api.bag.BagQueryConfig
Return a Map from a converter Class name (such as org.intermine.bio.web.logic.OrthologueConverter) to set of additional converters.
getAdditionalFields() - Method in class org.intermine.web.search.KeywordSearchResult
additional display field expressions
getAdditionalParameter(HttpServletRequest, String) - Static method in class org.intermine.web.logic.PortalHelper
Searches a request for additional parameters that might match an additional converter.
getAlgorithm() - Method in enum org.intermine.web.logic.widget.ErrorCorrection.Strategy
 
getAlias() - Method in class org.intermine.sql.query.AbstractTable
Returns the alias for this AbstractTable object.
getAlias() - Method in class org.intermine.sql.query.SelectValue
Gets the alias from this object.
getAliasedColumnHeaders(PathQuery, WebConfig) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
Get the view for a path query reformatted to obey the labels given in webconfig.
getAliases() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return all values of the Alias field from the attributes of this record.
getAliases() - Method in class org.intermine.objectstore.query.Query
Returns the map of QuerySelectables and FromElements to String aliases
getAll() - Method in class org.intermine.web.security.KeyStorePublicKeySource
 
getAll() - Method in interface org.intermine.web.security.PublicKeySource
 
getAllAttributeDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets all AttributeDescriptors for this class and its super classes - i.e. fields that are not references or collections.
getAllBags() - Method in class org.intermine.api.profile.Profile
Get all bags associated with this profile, both valid and invalid.
getAllChildren() - Method in class org.intermine.bio.chado.ChadoCVTerm
Return a Set of all the child ChadoCVTerms of this term.
getAllClassDescriptors() - Method in class org.intermine.xml.full.Item
Return the ClassDescriptors of the class of this Item (as given by className) and all the implementations.
getAllCollectionDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets all CollectionDescriptors for this class - i.e. including those from superclass.
getAllCVTerms() - Method in class org.intermine.bio.chado.ChadoCV
Return a Set of all the CVTerms in this CV.
getAlleleCVTermsResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Get result set of feature_id, cvterm_id pairs for the alleles in flybase chado.
getAllelePropPubResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Return a result set containing the featureprop_id and the publication identifier of the featureprops for al alleles.
getAllelePropResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Return a result set containing the alleles and their featureprops.
getAllFieldDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets the FieldDescriptors for this class and all superclasses and interfaces.
getAllGenomicRegionOverlapFeaturesByType(Map<GenomicRegion, List<List<String>>>, String) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Get a set of ids of all span's overlap features by given feature type. for GenomicRegionSearchAjaxAction use.
getAllJSONResults(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService
Returns all the results for the given template template, as JSON objects (see @link {http://www.intermine.org/wiki/JSONObjectFormat}).
getAllJSONResults(String) - Method in class org.intermine.webservice.client.services.QueryService
Fetch all the results as a list of JSON Objects
getAllJSONResults(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
Returns all the results for the given template template with the given parameters, as JSON objects (see @link {http://www.intermine.org/wiki/JSONObjectFormat}).
getAllNullAttributes() - Method in class org.intermine.objectstore.ObjectStoreSummary
Get a list of the attributes that are always null or empty.
getAllNullReferencesAndCollections() - Method in class org.intermine.objectstore.ObjectStoreSummary
Get a list of reference and collection names that are always null or empty.
getAllParents() - Method in class org.intermine.bio.chado.ChadoCVTerm
Return a Set of all the parent ChadoCVTerms of this term.
getAllParents() - Method in class org.intermine.bio.postprocess.PopulateChildFeatures
 
getAllPartOfs(String) - Method in class org.intermine.bio.ontology.SequenceOntology
 
getAllReferenceDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets all ReferenceDescriptors for this class - i.e. including those from superclass.
getAllReportDisplayersForType(String) - Method in class org.intermine.web.displayer.DisplayerManager
Get all displayers for the given type regardless of placement.
getAllResults(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService
Returns all the results for the given template template.
getAllResults(String) - Method in class org.intermine.webservice.client.services.QueryService
Returns all of the results of the specified PathQuery.
getAllResults(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
Returns all the results for the given template template with the given parameters.
getAllRowIterator(String) - Method in class org.intermine.webservice.client.services.QueryService
Returns all the results of a specified PathQuery as an iterator.
getAllRows() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return all the resultElementRows of the table as a List of Lists.
getAllRowsIterator(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService
Returns an iterator over all the rows for the template.
getAllRowsIterator(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
Returns all the rows for the template when run with the given parameters.
getAllSelected() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
getAllSelectedColumn() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
If a whole column is selected, return its index, otherwise return -1.
getAllSubs(ClassDescriptor) - Method in class org.intermine.metadata.Model
Get the ClassDescriptors for the all subclasses of a class
getAllSuperclassNames() - Method in class org.intermine.metadata.ClassDescriptor
Get the full inheritance list for this class.
getAllSuperDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Get the full inheritance list for this class.
getAllSuperUsers() - Method in class org.intermine.api.profile.ProfileManager
 
getAlteredViews(PathQuery) - Static method in class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj
Get the views for the transformed query.
getAnalysedTotal() - Method in class org.intermine.web.logic.widget.EnrichmentResults
Get the number of items in the sample that had an attribute value.
getAnnotatedCountsInPopulation() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
For each attribute give a count of items in the whole population that have that attribute assigned to them, M.
getAnnotatedCountsInPopulation() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
 
getAnnotatedCountsInSample() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
For each attribute give a count of items in the sample that have that attribute assigned to them, k.
getAnnotatedCountsInSample() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
 
getAPI() - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
getApiKey() - Method in class org.intermine.api.profile.Profile
 
getAPIVersion() - Method in class org.intermine.webservice.client.core.Service
 
getAppendConfig() - Method in class org.intermine.web.logic.config.HeaderConfigTitle
 
getApplicationName() - Method in class org.intermine.webservice.client.core.Service
 
getAppliedData(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return the rows needed for data from the applied_protocol_data table.
getAppliedDataAll(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return the rows needed for data from the applied_protocol_data table.
getAppliedDataAttributes(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Query to get data attributes.
getAppliedDataCharacteristics(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return the rows needed for data from the applied_protocol_data table.
getAppliedProtocols(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return the rows needed from the appliedProtocol table.
getApproximateType() - Method in class org.intermine.objectstore.query.QueryCast
Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.
getApproximateType() - Method in interface org.intermine.objectstore.query.QueryEvaluable
Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.
getApproximateType() - Method in class org.intermine.objectstore.query.QueryExpression
Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.
getApproximateType() - Method in class org.intermine.objectstore.query.QueryField
Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.
getApproximateType() - Method in class org.intermine.objectstore.query.QueryForeignKey
Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.
getApproximateType() - Method in class org.intermine.objectstore.query.QueryFunction
Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.
getApproximateType() - Method in class org.intermine.objectstore.query.QueryValue
Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.
getApproximateType() - Method in class org.intermine.objectstore.query.UnknownTypeValue
Returns the approximate type of the argument.
getArg1() - Method in class org.intermine.objectstore.query.ClassConstraint
Returns the QueryClass argument 1
getArg1() - Method in class org.intermine.objectstore.query.QueryExpression
Returns the left argument of the expression.
getArg1() - Method in class org.intermine.objectstore.query.SimpleConstraint
Returns the left argument of the constraint.
getArg2() - Method in class org.intermine.objectstore.query.QueryExpression
Returns the right argument, or the position argument of the substring.
getArg2() - Method in class org.intermine.objectstore.query.SimpleConstraint
Returns the right argument of the constraint.
getArg2Object() - Method in class org.intermine.objectstore.query.ClassConstraint
Returns the Object argument 2
getArg2QueryClass() - Method in class org.intermine.objectstore.query.ClassConstraint
Returns the QueryClass argument 2
getArg3() - Method in class org.intermine.objectstore.query.QueryExpression
Returns the length argument of a substring expression.
getAspect(String) - Static method in class org.intermine.api.tag.AspectTagUtil
Extracts aspect from tag name.
getAspectDisplayers() - Method in class org.intermine.web.logic.config.Type
 
getAspects() - Method in class org.intermine.web.logic.config.Displayer
Get the aspects of this displayer
getAspects(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Returns the Map of aspects.
getAspectSources() - Method in class org.intermine.web.logic.aspects.Aspect
Get the AspectSources.
getAspectTemplates(String) - Method in class org.intermine.api.template.TemplateManager
Get public templates for a particular aspect.
getAspectTemplates(String, Integer) - Method in class org.intermine.api.template.TemplateManager
Get public templates for a particular aspect.
getAttribute() - Method in class org.intermine.bio.dataconversion.UniprotEntry
the identifier is only held until the next line of the XML is processed, at which point the item is stored
getAttribute(String) - Static method in class org.intermine.web.context.InterMineContext
Get the value of a stored attribute.
getAttribute(String) - Method in class org.intermine.xml.full.Item
Get a named attribute.
GetAttributeAsFileAction - Class in org.intermine.web.struts
Provide an attribute value as a file
GetAttributeAsFileAction() - Constructor for class org.intermine.web.struts.GetAttributeAsFileAction
 
getAttributeDescriptorByName(String) - Method in class org.intermine.metadata.ClassDescriptor
Gets an AttributeDescriptor for a field of the given name.
getAttributeDescriptorByName(String, boolean) - Method in class org.intermine.metadata.ClassDescriptor
Gets an AttributeDescriptor for a field of the given name.
getAttributeDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets AttributeDescriptors for this class - i.e. fields that are not references or collections.
getAttributeDescriptors() - Method in class org.intermine.web.logic.results.ReportObject
Get attribute descriptors.
getAttributeIndexStatements(ClassDescriptor, Map<String, IndexStatement>) - Method in class org.intermine.task.CreateIndexesTask
Add indexes for all fields to the relevant tables for a given ClassDescriptor.
getAttributeOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of attributeOp
getAttributeOps() - Method in class org.intermine.web.struts.TemplateForm
Get the attribute ops
getAttributeOps(String) - Method in class org.intermine.web.struts.TemplateForm
Get an attribute op
getAttributeOptions() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of attributeValue
getAttributes() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the attributes of this record as a Map from attribute key to Lists of attribute values.
getAttributes() - Method in class org.intermine.objectstore.intermine.DatabaseSchema.Fields
Returns the Set of attributes
getAttributes() - Method in class org.intermine.web.logic.results.ReportObject
Get the attribute fields and values for this object
getAttributes() - Method in class org.intermine.xml.full.Item
Get all the attributes.
getAttributesFromBag(InterMineBag, ObjectStore, String, String, String) - Static method in class org.intermine.web.logic.bag.BagHelper
 
getAttributesFromBag(InterMineBag, ObjectStore, String, String) - Static method in class org.intermine.web.logic.bag.BagHelper
Used by esyn tool
getAttributeValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of attributeValue
getAttributeValues() - Method in class org.intermine.web.struts.TemplateForm
Get the attribute values
getAttributeValues(String) - Method in class org.intermine.web.struts.TemplateForm
Get an attribute value
getAuthenticatedUser() - Method in class org.intermine.webservice.server.WebService
Get a profile that is a true authenticated user that exists in the database.
getAutoCompleter() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return the autocompleter for this path if one is available.
getAutoCompleter(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the AutoCompleter stored on the ServletContext.
getAverage() - Method in class org.intermine.webservice.client.services.QueryService.NumericSummary
 
getBag(Profile, String) - Method in class org.intermine.api.bag.BagManager
Fetch a global or user or shared bag by name.
getBag() - Method in class org.intermine.api.bag.SharingInvite
 
getBag() - Method in class org.intermine.objectstore.query.BagConstraint
Get the bag Collection.
getBag() - Method in interface org.intermine.objectstore.query.ConstraintWithBag
Returns the bag that the constraint is using.
getBag() - Method in class org.intermine.objectstore.query.MultipleInBagConstraint
Returns the bag that this object was constructed with.
getBag() - Method in class org.intermine.objectstore.query.QueryClassBag
Returns the bag of objects.
getBag() - Method in class org.intermine.pathquery.PathConstraintBag
Returns the bag name that the constraint is constraining to.
getBag() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
the bag that this widget is using
getBag(String) - Method in class org.intermine.web.struts.TemplateForm
Get the bag name selected.
getBagConverter(InterMineAPI, WebConfig, String) - Static method in class org.intermine.web.logic.PortalHelper
Returns a BagConverter for the given parameters.
getBagCreationQuery() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return a Query that produces a Results object of the selected objects.
getBagDisplayers() - Method in class org.intermine.web.logic.config.Type
Get the List of bag Displayers
getBagId() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
getBagId() - Method in class org.intermine.objectstore.query.ObjectStoreBag
Returns the identifier of the bag.
getBagManager() - Method in interface org.intermine.api.API
 
getBagManager() - Method in class org.intermine.api.InterMineAPI
 
getBagManager() - Static method in class org.intermine.api.query.PathQueryAPI
Returns a BagManager.
getBagName() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
getBagName() - Method in class org.intermine.web.struts.FindInListForm
 
getBagName() - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Get the value of bagName
getBagName() - Method in class org.intermine.web.struts.WidgetForm
 
getBagName() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
Get the type of the bag
getBagNames() - Method in class org.intermine.pathquery.PathQuery
Returns all bag names used in constraints on this query.
getBagOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of bagOp
getBagOp(String) - Method in class org.intermine.web.struts.TemplateForm
Get the bag operation selected.
getBagOps() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return the valid constraint ops when constraining on a bag.
getBagQueries(String) - Method in class org.intermine.api.bag.BagQueryConfig
Return a list of BagQuerys to run for a given type
getBagQueries() - Method in class org.intermine.api.bag.BagQueryHandler
Return the bag queries from the XML file.
getBagQueryConfig() - Method in interface org.intermine.api.API
 
getBagQueryConfig() - Method in class org.intermine.api.bag.BagQueryHandler
Return the BagQueryConfig created from the XML.
getBagQueryConfig() - Method in class org.intermine.api.InterMineAPI
 
getBagQueryConfig() - Static method in class org.intermine.api.query.PathQueryAPI
Returns a BagQueryConfig configured in WEB-INF/bag-queries.xml.
getBagQueryResult() - Method in class org.intermine.api.bag.BagQueryUpgrade
 
getBagQueryRunner() - Method in interface org.intermine.api.API
 
getBagQueryRunner() - Method in class org.intermine.api.InterMineAPI
The bag-query runner is the object that performs look-up queries used when constructing bags from lists of identifiers, and in path-queries when LOOKUP constraints are used.
getBags(Profile) - Method in class org.intermine.api.bag.BagManager
Fetch all global bags, user bags and shared bags combined in the same map.
getBags() - Method in class org.intermine.api.bag.operations.BagOperation
 
getBags() - Method in class org.intermine.api.profile.BagSet
 
getBags() - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
Returns the List of bags.
getBags() - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject
Returns the Collection of bags.
getBags() - Method in class org.intermine.web.logic.query.DisplayConstraint
Get a list of public and user bag names available and currentfor this path.
getBagsAndClasses(Set<ClassDescriptor>, Set<InterMineBag>, Profile, BagManager, Model, String[]) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils
Given an array of bag names, populate both a set of bags, and a set of class-descriptors with the objects these names refer to.
getBagsOfType(Profile, String) - Method in class org.intermine.api.bag.BagManager
Fetch global and user bags of the specified type or a subclass of the specified type.
getBagsOfType(Profile, String, boolean) - Method in class org.intermine.api.bag.BagManager
Fetch global and user bags of the specified type or a subclass of the specified type.
getBagTableNames() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getBagType() - Method in class org.intermine.web.logic.query.DisplayConstraint
Returns the bag type that the constraint can be constrained to.
getBagType() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
getBagType() - Method in class org.intermine.web.struts.BagUploadConfirmForm
Get the bag type - hidden form value.
getBagType() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
getBagType() - Method in class org.intermine.web.struts.WidgetForm
 
getBagValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of bagValue
getBaseEof() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Returns the base equivalent object fetcher.
getBaseLink() - Method in class org.intermine.web.tags.table.NavigationBarTag
 
getBaseUrl() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
getBaseUrl(HttpServletRequest) - Static method in class org.intermine.web.logic.PortalHelper
Get the base url for this web-app.
getBaseURL() - Method in class org.intermine.web.util.AttributeLinkURL
 
getBaseURL() - Method in class org.intermine.web.util.URLGenerator
 
getBatch(int, boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches
Gets a batch by whatever means - maybe batches, maybe the ObjectStore.
getBatchFromCache(int) - Method in class org.intermine.objectstore.query.ResultsBatches
Returns the given batch, if it is already in the batch cache.
getBatchNoForRow(int) - Method in class org.intermine.objectstore.query.Results
Gets the batch for a particular row
getBatchNoForRow(int) - Method in class org.intermine.objectstore.query.ResultsBatches
Gets the batch for a particular row
getBatchSize() - Method in class org.intermine.objectstore.query.Results
Gets the batch size being used.
getBatchSize() - Method in class org.intermine.objectstore.query.ResultsBatches
Gets the batch size being used.
getBeanDescriptor() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getBeanDescriptor() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getBest() - Method in class org.intermine.sql.precompute.BestQueryExplainer
Gets the best Candidate found so far.
getBestExplainResult() - Method in class org.intermine.sql.precompute.BestQueryExplainer
Gets the ExpainResult for the best Query found so far.
getBestExplainResult() - Method in class org.intermine.sql.precompute.BestQueryFallback
Gets the ExpainResult for the best Query found so far
getBestQuery() - Method in class org.intermine.sql.precompute.BestQuery
Gets the best Query found so far
getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryExplainer
Gets the best Query found so far
getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryFallback
Gets the best Query found so far
getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryLogger
Gets the best Query found so far
getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryStorer
Gets the best Query found so far
getBestQuery() - Method in class org.intermine.sql.precompute.EncloseSubqueryBestQuery
Gets the best Query found so far
getBestQueryString() - Method in class org.intermine.sql.precompute.BestQuery
Gets the best query String found so far
getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryExplainer
Gets the best query String found so far.
getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryFallback
Gets the best query String found so far
getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryLogger
Gets the best query String found so far
getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryStorer
Gets the best query String found so far
getBestQueryString() - Method in class org.intermine.sql.precompute.EncloseSubqueryBestQuery
Gets the best query String found so far
getBgcolor() - Method in class org.intermine.api.mines.LocalMine
 
getBgcolor() - Method in interface org.intermine.api.mines.Mine
 
getBgcolor() - Method in class org.intermine.api.mines.RemoteMine
 
getBinaryIndexMap() - Method in class org.intermine.web.autocompletion.AutoCompleter
Returns byte array of the RAMIndexMap
getBinsParam() - Method in class org.intermine.objectstore.query.WidthBucketFunction
 
getBlockCount() - Method in class org.intermine.bio.io.bed.BEDRecord
 
getBlockCount() - Method in class org.intermine.bio.io.gaf.GAFRecord
 
getBlockSizes() - Method in class org.intermine.bio.io.bed.BEDRecord
 
getBlockSizes() - Method in class org.intermine.bio.io.gaf.GAFRecord
 
getBlockStarts() - Method in class org.intermine.bio.io.bed.BEDRecord
 
getBlockStarts() - Method in class org.intermine.bio.io.gaf.GAFRecord
 
getBoolean(String) - Method in class org.intermine.webservice.client.results.Item
Get a property known to be an boolean.
getBottomUpLevelTraversal() - Method in class org.intermine.metadata.Model
Return the classes in the model in level order from deepest to shallowest, the order of nodes at any given level is undefined.
getBuffer() - Method in class org.intermine.sql.writebatch.PostgresByteArrayOutputStream
Returns the byte buffer without copying it.
getBuildMode() - Method in class org.intermine.api.tracker.track.ListTrack
Return the way the list is built
getButton() - Method in class org.intermine.web.logic.query.MetadataNode
Gets the value of button
getByCells() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions
 
getByChadoId(Integer) - Method in class org.intermine.bio.chado.ChadoCV
Return the ChadoCVTerm object for a given cvterm_id.
getByLevel() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions
 
getByName() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions
 
getByName() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions
 
getByOrgan() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions
 
getByPValue() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions
 
getByPValue() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions
 
getByToken(InterMineAPI, String) - Static method in class org.intermine.api.bag.SharingInvite
 
getByTStatistic() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions
 
getByTStatistic() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions
 
getCallback() - Method in class org.intermine.webservice.server.WebService
Get the value of the callback parameter.
getCanCreateConstraint() - Method in class org.intermine.web.logic.query.MetadataNode
Returns true if there is any possibility of creating a constraint on this path.
getCandidateLoops(String) - Method in class org.intermine.pathquery.PathQuery
Returns the set of paths that could feasibly be loop constrained onto the given path, given the current outer join situation.
getCandidateLoops() - Method in class org.intermine.web.logic.query.DisplayConstraint
Returns the set of paths that could feasibly be loop constrained onto the constraint's path, given the query's outer join situation.
getCaseSensitive() - Method in interface org.intermine.api.idresolution.JobInput
 
getCaseSensitive() - Method in class org.intermine.web.logic.bag.WebJobInput
 
getCaseSensitive() - Method in class org.intermine.web.struts.BuildBagForm
 
getCategories(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Gets the aspect categories from the servlet context.
getCategory() - Method in class org.intermine.sql.precompute.PrecomputedTable
Returns the category of this PrecomputedTable
getCategoryPath() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
getCauseElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
getCauseElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
 
getCDNALengthResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Return a result set containing the feature_id and its seqlen The method is protected so that is can be overridden for testing.
getCDSs() - Method in class org.intermine.bio.web.model.GeneModel
Get the CDSs if present.
getChadoCV(String) - Method in class org.intermine.bio.chado.ChadoCVFactory
Get a new ChadoCV containing only cv terms from the cv with the given name.
getChadoDBConverter() - Method in class org.intermine.bio.dataconversion.ChadoProcessor
Return the ChadoDBConverter that was passed to the constructor.
getChadoIdToOrgDataMap() - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
Return a map from chado organism_id to OrganismData object for all the organisms that we are processing
getChadoOrganismIds(Connection) - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
Return a map from chado organism id to OrganismData for the organisms in the organism table in chado.
getCharSet() - Method in class org.intermine.webservice.client.core.ContentType
 
getChartType() - Method in class org.intermine.webservice.client.widget.Widget
 
getChartWidgets() - Method in class org.intermine.webservice.client.services.WidgetService
 
getChildId() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
Get childId value
getChildren() - Method in class org.intermine.pathquery.LogicExpression.Operator
Get an unmodifiable copy of the node's children.
getChildren(ClassDescriptor) - Static method in class org.intermine.web.struts.InitialiserPlugin
Get the names of the type of this ClassDescriptor and all its descendants
getChildren(ClassDescriptor, Set<String>) - Static method in class org.intermine.web.struts.InitialiserPlugin
Add the names of the descendents of a ClassDescriptor to a Set
getChildTermId() - Method in class org.intermine.bio.ontology.OboRelation
 
getChr() - Method in class org.intermine.bio.web.model.GenomicRegion
 
getChrLength() - Method in class org.intermine.bio.web.model.ChromosomeInfo
 
getChrom() - Method in class org.intermine.bio.io.bed.BEDRecord
 
getChrom() - Method in class org.intermine.bio.io.gaf.GAFRecord
 
getChromEnd() - Method in class org.intermine.bio.io.bed.BEDRecord
 
getChromEnd() - Method in class org.intermine.bio.io.gaf.GAFRecord
 
getChromosome(String, int) - Method in class org.intermine.bio.dataconversion.BioDBConverter
Make a Chromosome Item, then store and return it.
getChromosome(String, Organism) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask
Return a Chromosome object for the given item.
getChromosomeFeatureMap(Integer) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Fetch the populated map of chromosome-like features.
getChromosomeFeatureTypes() - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Get a list of the chado/so types of the Chromosome-like objects we wish to load.
getChromosomeInfo(InterMineAPI) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner
Query the information of all the organisms and their chromosomes' names and length.
getChromosomeInfo(InterMineAPI, int) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner
Query the information of all the organisms and their chromosomes' names and length.
getChromosomeInfomationMap() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Get chromosome information as in a map, keys are lowercased chromosome ids
getChromosomeStructureVariationResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Return the results of running a query for the chromosome_structure_variation feature types.
getChromStart() - Method in class org.intermine.bio.io.bed.BEDRecord
 
getChromStart() - Method in class org.intermine.bio.io.gaf.GAFRecord
 
getChrPID() - Method in class org.intermine.bio.web.model.ChromosomeInfo
 
getChrPIDLowerCase() - Method in class org.intermine.bio.web.model.ChromosomeInfo
 
getClass(String) - Static method in class org.intermine.metadata.TypeUtil
Instantiate a class by unqualified name The name should be "Date" or that of a primitive container class such as "Integer"
getClass(String, Model) - Static method in class org.intermine.metadata.TypeUtil
Instantiate a class by unqualified name The name should be "InterMineObject" or the name of class in the model provided
getClassConfig() - Method in class org.intermine.web.logic.config.FieldConfig
 
getClassCount(String) - Method in class org.intermine.objectstore.ObjectStoreSummary
Get the number of instances of a particular class in the ObjectStore.
getClassDescriptor() - Method in class org.intermine.metadata.FieldDescriptor
Get the ClassDescriptor for this field's class.
getClassDescriptor() - Method in class org.intermine.metadata.PrimaryKey
Return the ClassDescriptor for class this key is defined for
getClassDescriptor() - Method in class org.intermine.web.logic.results.ReportObject
Get the class descriptor for this object
getClassDescriptorByName(String) - Method in class org.intermine.metadata.Model
Get a ClassDescriptor by name, null if no ClassDescriptor of given name in Model.
getClassDescriptorByName(String) - Method in class org.intermine.xml.full.Item
Throw a RuntimeException if any of the named class isn't in the Model set by setModel().
getClassDescriptors() - Method in class org.intermine.api.profile.InterMineBag
Return the class descriptors for the type of this bag.
getClassDescriptors() - Method in class org.intermine.metadata.Model
Get all ClassDescriptors in this model.
getClassDescriptorsForClass(Class<?>) - Method in class org.intermine.metadata.Model
Takes a Class, and generates a Set of all ClassDescriptors that are the Class or any of its parents.
getClasses() - Method in class org.intermine.api.bag.operations.BagOperation
 
getClasses() - Method in class org.intermine.metadata.Model.ModelAST
 
getClassesForBags(Collection<InterMineBag>) - Method in class org.intermine.webservice.server.lists.AbstractListService
Get the classes represented by a collection of bags.
getClassFieldConfigs(WebConfig, ClassDescriptor) - Static method in class org.intermine.web.logic.config.FieldConfigHelper
Find the FieldConfig objects for the the given ClassDescriptor (or generate them).
getClassFieldConfigs(ClassDescriptor) - Method in class org.intermine.web.logic.results.InlineResultsTable
Find the FieldConfig objects for the the given ClassDescriptor.
getClassFromString(String) - Static method in class org.intermine.metadata.Util
Returns the class (not primitive) associated with the given String type.
getClassIndex(List<Class<?>>, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper
 
getClassIndexes(List<Class<?>>, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper
 
getClassKeys() - Method in interface org.intermine.api.API
 
getClassKeys() - Method in class org.intermine.api.bag.operations.BagOperation
 
getClassKeys() - Method in class org.intermine.api.InterMineAPI
The class keys are the list of fields used to identify objects in the data base, so for Employee it would include "name", and for Gene it would include "symbol".
getClassKeys() - Static method in class org.intermine.api.query.PathQueryAPI
Returns classkeys configured in class_keys.properties.
getClassKeys() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
Get the classKeys
getClassName() - Method in class org.intermine.api.bag.AdditionalConverter
 
getClassName() - Method in class org.intermine.bio.chado.config.CreateCollectionAction
Return the className that was passed to the constructor.
getClassName() - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
Return the class name set with setClassName().
getClassName() - Method in class org.intermine.web.autocompletion.LuceneObjectClass
getClassName
getClassName() - Method in class org.intermine.web.logic.config.TableExportConfig
Get the class name of the exporter eg. org.intermine.bio.web.export.SequenceHttpExporter
getClassName() - Method in class org.intermine.web.logic.config.Type
Get the class name
getClassName() - Method in class org.intermine.web.logic.results.InlineResultsTableRow
 
getClassName() - Method in class org.intermine.web.logic.results.InlineTableResultElement
 
getClassName() - Method in class org.intermine.web.struts.QueryClassSelectForm
Get the class name
getClassName() - Method in class org.intermine.xml.full.Item
Get the class name of this item.
getClassName(Object, Model) - Static method in class org.intermine.xml.XmlHelper
Get the class name if object represents a material class in model.
getClassNames() - Method in class org.intermine.bio.dataconversion.IdResolver
Return a set of class names the reslover holds
getClassNames() - Method in class org.intermine.metadata.Model
Get a Set of fully qualified class names in this model (i.e. including package name).
getClassNames(ObjectStore, String) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil
Given a String, perform a one of a set of expansions and return a Set of unqualified class names.
getClazz() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionType
 
getClazz() - Method in class org.intermine.objectstore.querygen.QueryGenUtil.QueryAndClass
Returns the class.
getClientId() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
 
getClientId() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
 
getClientId() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
 
getClientSecret() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
 
getClientSecret() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
 
getClientSecret() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
 
getClob() - Method in class org.intermine.objectstore.query.ClobAccess
Return the Clob that this object is accessing.
getClob() - Method in class org.intermine.objectstore.query.PendingClob
Return the Clob that this object is accessing.
getClobId() - Method in class org.intermine.objectstore.query.Clob
Returns the identifier of the Clob.
getCode() - Method in class org.intermine.web.logic.query.DisplayConstraint
If editing an existing constraint get the code for this constraint in the query, return null if creating a new constraint.
getCode() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
Get the code associated with this constraint in the query.
getCode() - Method in class org.intermine.web.logic.template.ConstraintInput
 
getCode() - Method in class org.intermine.webservice.client.template.TemplateParameter
 
getCode(String) - Static method in class org.intermine.webservice.server.CodeTranslator
Returns corresponding code of translated operation.
getCode() - Method in class org.intermine.webservice.server.output.Output
Gets the error code
getCollection() - Method in class org.intermine.web.logic.results.DisplayCollection
 
getCollection() - Method in class org.intermine.web.logic.results.ReportInList
 
getCollection(String) - Method in class org.intermine.webservice.client.results.Item
Get a set of items representing the elements in a collection field on an item.
getCollection(String) - Method in class org.intermine.xml.full.Item
Get a named collection.
getCollectionDescriptorByName(String) - Method in class org.intermine.metadata.ClassDescriptor
Gets a CollectionDescriptor for a collection of the given name.
getCollectionDescriptorByName(String, boolean) - Method in class org.intermine.metadata.ClassDescriptor
Gets a CollectionDescriptor for a field of the given name.
getCollectionDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets CollectionDescriptors for this class.
getCollections() - Method in class org.intermine.web.logic.results.ReportObject
Get the collection fields and values for this object
getCollections() - Method in class org.intermine.xml.full.Item
Get all the collections.
getCollectionsForClass(Class<?>) - Method in class org.intermine.metadata.Model
Takes a Class, and generates a Map of all the collections that are in the Class or any of its parents.
getColNames() - Method in class org.intermine.sql.writebatch.TableBatch
Returns the column names.
getColumn() - Method in class org.intermine.webservice.client.services.QueryService.NumericSummary
 
getColumnAliases(Query) - Static method in class org.intermine.objectstore.query.QueryHelper
Returns a list of aliases, where each alias corresponds to each element of the SELECT list of the Query object.
getColumnClasses(PagedTable) - Static method in class org.intermine.web.logic.export.ExportHelper
 
getColumnFieldClasses() - Method in class org.intermine.task.DelimitedFileConfiguration
Return a List of Class objects corresponding to the fields returned by getColumnFieldDescriptors().
getColumnFieldDescriptors() - Method in class org.intermine.task.DelimitedFileConfiguration
Return a List of the configured AttributeDescriptors.
getColumnHeaders() - Method in class org.intermine.pathquery.PathQuery
Returns the paths descriptions for the view.
getColumnHeaderStyle() - Method in class org.intermine.webservice.server.WebService
Get an enum which represents the column header style (path, friendly, or none)
getColumnId() - Method in class org.intermine.api.results.Column
 
getColumnIdentifier() - Method in class org.intermine.api.results.Column
Used in the view to match this element
getColumnName(FieldDescriptor) - Static method in class org.intermine.sql.DatabaseUtil
Creates a column name for a field descriptor
getColumnNames() - Method in class org.intermine.api.results.WebResults
Return the names of the columns of the results.
getColumnNames() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return the column names
getColumnNames() - Method in class org.intermine.web.tags.table.TableTag
 
getColumnPaths(PagedTable) - Static method in class org.intermine.web.logic.export.ExportHelper
Return a List containing the Path objects from the Columns of this PagedTable.
getColumns() - Method in class org.intermine.api.results.ExportResultsIterator
Allows test to access column info.
getColumns() - Method in class org.intermine.api.results.WebResults
Returns the columns for these results.
getColumns() - Method in interface org.intermine.api.results.WebTable
Returns the Column objects for this table.
getColumns() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the list of column configurations
getColumns() - Method in class org.intermine.web.logic.widget.TableWidget
Get the columns
getColumns() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
Get the columnNames
getColumns() - Method in class org.intermine.webservice.server.core.SubTable
 
getColumnsPath() - Method in class org.intermine.api.results.WebResults
 
getColumnsPath() - Method in interface org.intermine.api.results.WebTable
 
getColumnsSize() - Method in class org.intermine.web.logic.results.InlineResultsTable
 
getColumnSummary(String, String) - Static method in class org.intermine.dwr.AjaxServices
Get the summary for the given column
getColumnTitle() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
getColumnTypes(Query) - Static method in class org.intermine.objectstore.query.QueryHelper
Returns a list of Class objects, where each object corresponds to the type of each element of the SELECT list of the Query object.
getColumnTypeString(Class<?>) - Method in class org.intermine.sql.Database
Return the SQL type used to store objects of the given Class.
getCommand(String, Map<String, String>) - Static method in class org.intermine.webservice.server.jbrowse.Commands
return null if not a suitable command.
getComment() - Method in class org.intermine.template.TemplateQuery
Get the private comment for this template.
getComment() - Method in class org.intermine.web.struts.TemplateSettingsForm
Return the comment
getCommentEvidence() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getComments() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getCommentType() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getCommonFeaturesMap() - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Get a map of features that are expected to be common between submissions.
getCommonJsonConstraintPrefix(String, PathConstraint) - Method in class org.intermine.pathquery.PathQuery
Get the JSON prefix common to all constraints.
getCommonJsonConstraintPrefix(String, PathConstraint) - Method in class org.intermine.template.TemplateQuery
 
getCompatibleCurrentBags(Profile, String) - Method in class org.intermine.api.bag.BagManager
Fetch global and user bags current of the specified type or a subclass or any superclass of the specified type.
getComplete() - Method in class org.intermine.objectstore.query.ResultsInfo
Returns the estimated amount of time taken to produce the entire set of results.
getComplete() - Method in class org.intermine.sql.query.ExplainResult
Returns the number of page requests before the query is completed, estimated by the database for this query.
getCompletedProcessors() - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
 
getComplex(String) - Method in class org.intermine.webservice.server.complexes.ExportService
 
getComponents() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getComponentsForQuery(Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Returns a Set of independent components that affect the results of the given Query.
getComponentsForQuery(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Returns a Set of independent components that affect the results of the given Query.
getComponentsForQuery(Query) - Method in interface org.intermine.objectstore.ObjectStore
Returns a Set of independent components that affect the results of the given Query.
getComponentsForQuery(Query) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Returns a Set of independent components that affect the results of the given Query.
getComponentsForQuery(Query) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Returns a Set of independent components that affect the results of the given Query.
getComponentsForQuery(Query) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Returns a Set of independent components that affect the results of the given Query.
getConfig(int) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Return the config Map.
getConfig(int) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Return the config Map.
getConfig(int) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return the config Map.
getConfig(int) - Method in class org.intermine.bio.dataconversion.WormBaseProcessor
Return the config Map.
getConfig(String) - Method in class org.intermine.web.logic.export.http.TableExporterFactory
Return the TableExportConfig for the given id.
getConfigClassDescriptor() - Method in class org.intermine.task.DelimitedFileConfiguration
Return the ClassDescriptor of the class to modify.
getConfigId() - Method in class org.intermine.web.logic.widget.Widget
Get the ID of the corresponding WidgetConfig
getConfiguredTypes() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the unqualified class names for which this displayer should be displayed.
getConnectField() - Method in class org.intermine.api.bag.BagQueryConfig
Return the connecting field.
getConnection() - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
Get the connection to use when processing.
getConnection() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Returns a Connection.
getConnection() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Returns a Connection.
getConnection() - Method in class org.intermine.sql.Database
Gets a Connection to this Database
getConstrainField() - Method in class org.intermine.api.bag.BagQueryConfig
Return the constrain field.
getConstraint() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
 
getConstraint() - Method in class org.intermine.objectstore.query.Query
Get the current constraint on this Query
getConstraint() - Method in interface org.intermine.objectstore.query.Queryable
Returns the additional constraint.
getConstraint() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the additional constraint.
getConstraint() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Returns the additional constraint.
getConstraint() - Method in class org.intermine.sql.query.NotConstraint
Returns the contained constraint.
getConstraint() - Method in class org.intermine.template.TemplateValue
Returns the constraint that this object was constructed with.
getConstraintCodes() - Method in class org.intermine.pathquery.PathQuery
Return the constraint codes used in the query, some constraint types (subclasses) don't get assigned a code, these are not included.
getConstraintDescription(PathConstraint) - Method in class org.intermine.template.TemplateQuery
Returns the description attached to the given constraint.
getConstraintDescriptions() - Method in class org.intermine.template.TemplateQuery
Returns the constraint descriptions for this query.
getConstraintForCode(String) - Method in class org.intermine.pathquery.PathQuery
Returns the PathConstraint associated with a given code.
getConstraintGroups() - Method in class org.intermine.pathquery.PathQuery
Returns the outer join constraint codes groups map for this query, if the query verifies correctly.
getConstraintLogic() - Static method in class org.intermine.dwr.AjaxServices
Get the grouped constraint logic
getConstraintLogic() - Method in class org.intermine.pathquery.PathQuery
Returns the current constraint logic.
getConstraintLogicForEditableConstraints() - Method in class org.intermine.template.TemplateQuery
Return the constraint logic modified to contain only the blocks with editable constraints
getConstraintLogicForGroup(String) - Method in class org.intermine.pathquery.PathQuery
Returns the constraint logic for the given outer join group, if the query verifies correctly.
getConstraintOp(String) - Static method in class org.intermine.metadata.ConstraintOp
Get ConstraintOp for given operation code.
getConstraintOp() - Method in class org.intermine.web.logic.template.ConstraintInput
Returns constraint operation
getConstraintPath() - Method in class org.intermine.api.bag.AdditionalConverter
 
getConstraints() - Method in class org.intermine.objectstore.query.ConstraintSet
Returns the Set of constraints.
getConstraints() - Method in class org.intermine.pathquery.PathQuery
Returns a Map of all the constraints in this query, from PathConstraint to the constraint code used in the constraint logic.
getConstraints() - Method in class org.intermine.sql.query.ConstraintSet
Returns the Set of constraints forming this object.
getConstraints() - Method in class org.intermine.web.logic.querybuilder.SummaryPath
Return summary representations of constraints on this path or an empty list if none exist.
getConstraints() - Method in class org.intermine.web.logic.template.TemplateResultInput
Returns constraints.
getConstraintsForPath(String) - Method in class org.intermine.pathquery.PathQuery
Returns a list of PathConstraints applied to a given path or an empty list.
getConstraintSwitchOffAbility() - Method in class org.intermine.template.TemplateQuery
Returns the constraint SwitchOffAbility for this query.
getContainsOptions() - Method in class org.intermine.api.query.range.AbstractHelper
By default the CONTAINS options are same as the WITHIN options with the left and right operators swapped.
getContent(String, boolean, String, String) - Method in class org.intermine.dwr.AjaxServices
 
getContent() - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig
Get the content of the widget.
getContents() - Method in class org.intermine.api.profile.InterMineBag
Returns a List of BagValue (key field value and extra value) of the objects contained by this bag.
getContents() - Method in class org.intermine.api.profile.StorableBag
Returns a List of BagValue (key field value and extra value) of the objects contained by this bag.
getContentsAsIds() - Method in class org.intermine.api.profile.InterMineBag
Returns a List which contains the contents of this bag as Integer IDs.
getContentsOrderByExtraValue() - Method in class org.intermine.api.profile.StorableBag
 
getContentType() - Method in class org.intermine.bio.webservice.AbstractRegionExportService
 
getContentType() - Method in class org.intermine.bio.webservice.BEDQueryService
 
getContentType() - Method in class org.intermine.bio.webservice.BioQueryService
 
getContentType() - Method in class org.intermine.bio.webservice.FastaQueryService
 
getContentType() - Method in class org.intermine.bio.webservice.GAFQueryService
 
getContentType() - Method in class org.intermine.bio.webservice.GenomicRegionBedService
 
getContentType() - Method in class org.intermine.bio.webservice.GenomicRegionFastaService
 
getContentType() - Method in class org.intermine.bio.webservice.GenomicRegionGFF3Service
 
getContentType() - Method in class org.intermine.bio.webservice.GFFQueryService
 
getContentType() - Method in interface org.intermine.webservice.client.core.Request
 
getContentType() - Method in class org.intermine.webservice.client.core.RequestImpl
getContentType() - Method in enum org.intermine.webservice.server.Format
 
getConversionMapQuery(List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, Object) - Static method in class org.intermine.api.bag.TypeConverter
Get conversion query for the types provided, edited so that the first type is constrained to be in the bag.
getConversionQuery(List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, Object) - Static method in class org.intermine.api.bag.TypeConverter
Get conversion query for the types provided, edited so that the first type is constrained to be in the bag and the first type is removed from the view list so that the query only returns the converted type.
getConversionTemplates() - Method in class org.intermine.api.bag.BagQueryRunner
Fetch conversion template queries from the template manager.
getConversionTemplates(List<ApiTemplate>, Class) - Static method in class org.intermine.api.bag.TypeConverter
Return a Map from typeB to a TemplateQuery that will convert from typeA to typeB.
getConversionTemplates() - Method in class org.intermine.api.template.TemplateManager
Return template queries used for converting between types in bag upload and lookup queries, these are Superuser templates that have been tagged with TagNames.IM_CONVERTER.
getConvertCountForBag(String, String) - Static method in class org.intermine.dwr.AjaxServices
For a given bag name and a type different from the bag type, give the number of converted objects
getConvertedObjectIds(Profile, String, List<Integer>, String) - Method in class org.intermine.bio.web.logic.OrthologueConverter
runs the orthologue conversion pathquery and returns list of intermine IDs used in the portal
getConvertedObjectIds(Profile, String, List<Integer>, String) - Method in class org.intermine.web.logic.bag.BagConverter
 
getConvertedObjectMap(List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, Object, ObjectStore) - Static method in class org.intermine.api.bag.TypeConverter
Converts a List of objects from one type to another type using a TemplateQuery, returns a map from an original object to the converted object(s).
getConvertedObjects(HttpSession, List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, InterMineBag) - Static method in class org.intermine.web.logic.bag.BagConversionHelper
Converts a List of objects from one type to another type using a TemplateQuery, returns the converted objects.
getConvertedValue(Class<?>) - Method in class org.intermine.objectstore.query.UnknownTypeValue
Returns the value, converted (if possible) into the object type given by the input class.
getCorrection() - Method in interface org.intermine.web.logic.widget.EnrichmentOptions
 
getCorrection() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
getCorrectionCoefficient() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getCount() - Method in class org.intermine.api.profile.TagHandler
Return a count of the number of tags read.
getCount() - Method in class org.intermine.api.tracker.track.ListTrack
Return the number of items contained into the list
getCount() - Method in class org.intermine.web.logic.results.ReportInList
 
getCount() - Method in class org.intermine.web.logic.session.QueryCountQueryMonitor
Return the count set with setCount().
getCount(PathQuery) - Method in class org.intermine.webservice.client.services.QueryService
 
getCount(String) - Method in class org.intermine.webservice.client.services.QueryService
Returns the number of results the specified query will return.
getCount(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
Returns the number of results the specified template will return.
getCount(TemplateQuery) - Method in class org.intermine.webservice.client.services.TemplateService
 
getCountItemsWithLengthNotNull() - Method in class org.intermine.api.profile.InterMineBag
Return the number of items contained in the bag with length not null If the type bag is not a subclass of SequenceFeature, return 0
getCounts(Profile, InterMineBag) - Method in class org.intermine.bio.web.logic.OrthologueConverter
Method to return list of values and the counts of converted objects for that object used for display on list analysis page.
getCounts(Profile, InterMineBag) - Method in class org.intermine.web.logic.bag.BagConverter
Method to return list of values and the counts of converted objects for that object used for display on list analysis page.
getCounts() - Method in class org.intermine.web.logic.widget.EnrichmentResults
Get the count of each attribute value found in the sample.
getCreatedAt() - Method in class org.intermine.api.bag.SharingInvite
 
getCreatedAt() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
getCreatedAt() - Method in class org.intermine.webservice.client.lists.ItemList
Get the date when this list was created.
getCrossReferences() - Method in class org.intermine.bio.dataconversion.UniprotConfig
 
getCurrentBags(Profile) - Method in class org.intermine.api.bag.BagManager
Get the bags this user has access to, as long as they are current.
getCurrentBagsContainingId(Profile, Integer) - Method in class org.intermine.api.bag.BagManager
Fetch the current user or global or shared bags that contain the given id.
getCurrentBagsOfType(Profile, String) - Method in class org.intermine.api.bag.BagManager
Fetch global and user bags current of the specified type or a subclass of the specified type.
getCurrentFile() - Method in class org.intermine.dataconversion.FileConverter
Return the File that is currently being converted.
getCurrentPage() - Method in class org.intermine.web.tags.table.NavigationBarTag
 
getCurrentSavedBags() - Method in class org.intermine.api.profile.Profile
Get the value of savedBags current
getCurrentSelectedIdStrings() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return selected object ids of the current page as a String[], needed for jsp multibox.
getCurrentSelectedIdStringsList() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return selected object ids of the current page as a List.
getCurrentUserBagsOfType(Profile, String) - Method in class org.intermine.api.bag.BagManager
Fetch user bags current of the specified type or a subclass of the specified type.
getCustomConverterCounts(String, String) - Static method in class org.intermine.dwr.AjaxServices
For a list and a converter, return types and related counts
getCvName() - Method in class org.intermine.bio.chado.ChadoCV
Return the cvName that was passed to the constructor.
getCVTermRelationshipResultSet(Connection, String) - Method in class org.intermine.bio.chado.ChadoCVFactory
Return the rows from the cvterm_relationship table that relate cvterms from the cv with the given name.
getCVTermResultSet(Connection, String) - Method in class org.intermine.bio.chado.ChadoCVFactory
Return the rows from the cvterm table that are from the cv with the given name.
getDAG(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return the rows needed to construct the DAG of the data/protocols.
getData() - Method in class org.intermine.webservice.client.results.RowResultSet
 
getData() - Method in class org.intermine.webservice.client.results.TabTableResult
Get the raw data from this result set.
getData() - Method in class org.intermine.webservice.client.results.XMLTableResult
 
getDatabase() - Method in class org.intermine.bio.dataconversion.ChadoProcessor
Return the database to read from
getDatabase() - Method in class org.intermine.dataconversion.DBConverter
Get the Database that was passed to the constructor.
getDatabase() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Returns the Database used by this ObjectStore
getDatabase(String) - Static method in class org.intermine.sql.DatabaseFactory
Returns a connection to the named database
getDataSet(String, String) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter
Return a DataSet item with the given details.
getDataSet(String, String) - Method in class org.intermine.bio.dataconversion.BioFileConverter
Return a DataSet ref with the given details.
getDataSet() - Method in class org.intermine.bio.dataconversion.EnsembSnpLoaderTask
Get and store() the DataSet object to reference when creating new objects.
getDataSet() - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
Return the DataSet to add to each object.
getDataSet() - Method in class org.intermine.bio.dataconversion.GFF3Converter
Return the DataSet Item created for this GFF3Converter from the data set title passed to the constructor.
getDataSet() - Method in class org.intermine.bio.dataconversion.VcfLoaderTask
Get and store() the DataSet object to reference when creating new objects.
getDataSetItem(int) - Method in class org.intermine.bio.dataconversion.BioDBConverter
Return the DataSet Item created from the dataSetTitle.
getDataSetItem(String, Item) - Method in class org.intermine.bio.dataconversion.BioDBConverter
Return a DataSource item for the given name
getDataSetItem(String, String, String, Item) - Method in class org.intermine.bio.dataconversion.BioDBConverter
Return a DataSource item with the given details.
getDataSetItem(int) - Method in class org.intermine.bio.dataconversion.GenomeDBConverter
Return the DataSet Item created from the dataSetTitle.
getDataSetItem(String, String, String, Item) - Method in class org.intermine.bio.dataconversion.GFF3Converter
Return a DataSource item with the given details.
getDataSetReferenceList() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Return a ReferenceList containing the DataSet Items ids set by addDataSet()
getDatasetRefId() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getDataSetTitle(int) - Method in class org.intermine.bio.dataconversion.BioDBConverter
Return the DataSet title for a given taxon id.
getDataSetTitle(int) - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
Default implementation that makes a data set title based on the data source name.
getDataSetTitle(int) - Method in class org.intermine.bio.dataconversion.EnsemblGwasDbConverter
Return the DataSet title for a given taxon id.
getDataSetTitle(int) - Method in class org.intermine.bio.dataconversion.EnsemblSnpDbConverter
Return the DataSet title for a given taxon id.
getDataSetTitle(int) - Method in class org.intermine.bio.dataconversion.GenomeDBConverter
Default implementation that makes a data set title based on the data source name.
getDataSource(String) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter
Return a DataSource item for the given title
getDataSource(String) - Method in class org.intermine.bio.dataconversion.BioFileConverter
Return a DataSource item for the given title
getDataSource() - Method in class org.intermine.bio.dataconversion.EnsembSnpLoaderTask
Get and store() the DataSource object to reference when creating new objects.
getDataSource() - Method in class org.intermine.bio.dataconversion.GFF3Converter
Return the DataSource Item created for this GFF3Converter from the data source name passed to the constructor.
getDataSource() - Method in class org.intermine.bio.dataconversion.VcfLoaderTask
Get and store() the DataSource object to reference when creating new objects.
getDataSource() - Method in class org.intermine.sql.Database
Gets the DataSource object for this Database
getDataSourceItem() - Method in class org.intermine.bio.dataconversion.BioDBConverter
Return the DataSource Item created from the dataSourceName.
getDataSourceItem(String) - Method in class org.intermine.bio.dataconversion.BioDBConverter
Return a DataSet item for the given title
getDataSourceItem(String) - Method in class org.intermine.bio.dataconversion.GFF3Converter
Return a DataSet item for the given title
getDataSourceName() - Method in class org.intermine.bio.dataconversion.BioDBConverter
Return the data source name set by setDataSourceName().
getDataTracker() - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Returns the data tracker being used.
getDateCreated() - Method in class org.intermine.api.profile.InterMineBag
Return the creation date that was passed to the constructor.
getDateCreated() - Method in class org.intermine.api.profile.InvalidBag
 
getDateCreated() - Method in class org.intermine.api.profile.SavedQuery
Get the date on which the query was created.
getDateCreated() - Method in class org.intermine.api.profile.StorableBag
Get the date that this bag was created at.
getDayToken() - Method in class org.intermine.api.profile.Profile
Get a token with at least an hour of validity, and up to 24 hours.
getDayToken() - Method in class org.intermine.api.util.AnonProfile
 
getDb() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getDbDescription() - Method in class org.intermine.bio.util.ClobAccessReverseComplement
Returns a String that describes this object sufficiently for it to be recreated given an ObjectStore.
getDbDescription() - Method in class org.intermine.objectstore.query.ClobAccess
Returns a String that describes this object sufficiently for it to be recreated given an ObjectStore.
getDbDescription() - Method in class org.intermine.objectstore.query.PendingClob
Returns a String that describes this object sufficiently for it to be recreated given an ObjectStore.
getDbref() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getDbrefs() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getDbxrefResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return the interesting rows from the dbxref table.
getDbxrefs() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the first value of the Dbxref field from the attributes of this record.
getDefaultClass() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the QueryClass that represents the collection in this object.
getDefaultClass() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Returns the QueryClass that represents the collection in this object.
getDefaultEventIndex() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getDefaultEventIndex() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getDefaultFileName() - Method in class org.intermine.bio.webservice.AbstractRegionExportService
 
getDefaultFileName() - Method in class org.intermine.bio.webservice.BioQueryService
 
getDefaultFileName() - Method in class org.intermine.webservice.server.query.CodeService
 
getDefaultFileName() - Method in class org.intermine.webservice.server.query.QueryRetrieverService
 
getDefaultFileName() - Method in class org.intermine.webservice.server.SchemaListService
 
getDefaultFileName() - Method in class org.intermine.webservice.server.SummaryService
 
getDefaultFileName() - Method in class org.intermine.webservice.server.WebService
 
getDefaultFilterValue(WidgetConfig, InterMineBag) - Method in class org.intermine.webservice.server.widget.WidgetService
Get the default filter value for a widget.
getDefaultFormat() - Method in class org.intermine.bio.webservice.AbstractRegionExportService
 
getDefaultFormat() - Method in class org.intermine.bio.webservice.BioQueryService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.core.JSONService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.lists.AvailableListsService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.lists.ListMakerService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.model.ModelService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.path.PossibleValuesService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.query.CodeService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.query.QueryRetrieverService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.query.QueryToListService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.query.QueryUploadService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.query.result.QueryResultService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.query.result.TableRowService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.template.AvailableTemplatesService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.user.DeregistrationService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.VersionService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.WebService
 
getDefaultOperator(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the default operator to apply to new constraints.
getDefaultOutput(PrintWriter, OutputStream, String) - Method in class org.intermine.bio.webservice.AbstractRegionExportService
 
getDefaultOutput(PrintWriter, OutputStream, String) - Method in class org.intermine.bio.webservice.BioQueryService
 
getDefaultOutput(PrintWriter, OutputStream, String) - Method in class org.intermine.webservice.server.WebService
Make the default output for this service.
getDefaultOutput(PrintWriter, OutputStream) - Method in class org.intermine.webservice.server.WebService
Make the default output for this service.
getDefaultPermission(Profile) - Static method in class org.intermine.api.profile.ProfileManager
Wrap a profile in the default permission level.
getDefaultPropertyIndex() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getDefaultPropertyIndex() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
Returns default style class.
getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureBodyTag
Returns default style class.
getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureDetailsTag
Returns default style class.
getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureHeadTag
Returns default style class.
getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Returns default style class.
getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureTitleTag
Returns default style class.
getDefaultValue() - Method in class org.intermine.api.mines.LocalMine
 
getDefaultValue() - Method in interface org.intermine.api.mines.Mine
get first default value. used in querybuilder to select default extra value
getDefaultValue() - Method in class org.intermine.api.mines.RemoteMine
 
getDefaultValues() - Method in class org.intermine.api.mines.LocalMine
 
getDefaultValues() - Method in interface org.intermine.api.mines.Mine
 
getDefaultValues() - Method in class org.intermine.api.mines.RemoteMine
 
getDefaultViewForClass(String, Model, WebConfig, String) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
Return a list of string paths that are defined as WebConfig to be shown in results.
getDefaultViewForClass(String, Model, WebConfig) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
Return a list of string paths that are defined as WebConfig to be shown in results.
getDeleted(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return deleted subs in the chado db.
getDeletedClasses() - Method in class org.intermine.api.profile.ModelUpdate
Return a set containing all the deleted classes
getDeletionLocationResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Return a result set containing location for deletions (chromosome_structure_variation) objects.
getDescr() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
getDescription() - Method in class org.intermine.api.mines.LocalMine
 
getDescription() - Method in interface org.intermine.api.mines.Mine
 
getDescription() - Method in class org.intermine.api.mines.RemoteMine
 
getDescription() - Method in class org.intermine.api.profile.InterMineBag
Return the description of this bag.
getDescription() - Method in class org.intermine.api.profile.InvalidBag
 
getDescription() - Method in class org.intermine.api.profile.StorableBag
 
getDescription() - Method in interface org.intermine.api.search.WebSearchable
Return the description of this object.
getDescription() - Method in class org.intermine.bio.ontology.OboTerm
Get the term description.
getDescription(String) - Method in class org.intermine.pathquery.PathQuery
Returns the description for a given path, or null if no description is registered.
getDescription() - Method in class org.intermine.pathquery.PathQuery
Gets the description for this PathQuery.
getDescription() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return the label associated with a constraint if editing a template query constraint.
getDescription() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
Get the description for a constraint.
getDescription() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getDescription() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
Get the description
getDescription() - Method in class org.intermine.web.struts.TemplateSettingsForm
Return the description.
getDescription() - Method in class org.intermine.webservice.client.lists.ItemList
 
getDescription() - Method in class org.intermine.webservice.client.widget.Widget
 
getDescription() - Method in class org.intermine.webservice.server.lists.ListInput
 
getDescription(int) - Static method in class org.intermine.webservice.server.StatusDictionary
 
getDescriptions() - Method in class org.intermine.pathquery.PathQuery
Returns an unmodifiable Map which is a copy of the current set of path descriptions of this query at the time of execution of this method.
getDescriptiveString() - Method in class org.intermine.pathquery.PathConstraintLoop
Returns a descriptive string for this constraint, mainly useful for checking uniqueness.
getDescriptor() - Method in class org.intermine.web.logic.results.DisplayCollection
Get ReferenceDescriptor for this reference.
getDescriptor() - Method in class org.intermine.web.logic.results.DisplayReference
Get ReferenceDescriptor for this reference.
getDescriptor() - Method in class org.intermine.web.logic.results.InlineList
 
getDescriptors(Model) - Static method in class org.intermine.dataloader.DataLoaderHelper
Build a map from class and field names to a priority-ordered List of source name Strings.
getDirectChildren() - Method in class org.intermine.bio.chado.ChadoCVTerm
Get the direct children of this term.
getDirectDataLoader() - Method in class org.intermine.task.DirectDataLoaderTask
Return the DirectDataLoader for this Task.
getDirection() - Method in class org.intermine.pathquery.OrderElement
Returns the order direction of this OrderElement.
getDirectParents() - Method in class org.intermine.bio.chado.ChadoCVTerm
Get the direct parents of this term.
getDirectSubs(ClassDescriptor) - Method in class org.intermine.metadata.Model
Get the ClassDescriptors for the direct subclasses of a class
getDisableResultsCache() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets the disableResultsCache configuration option.
getDisableResultsCache() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Gets the disableResultsCache configuration option.
getDisplayer() - Method in class org.intermine.web.logic.config.FieldConfig
Get the displayer for that field
getDisplayerName() - Method in class org.intermine.web.displayer.ReportDisplayer
Gimme my name
getDisplayerPage() - Method in class org.intermine.web.logic.results.ReportObjectField
Return path to a custom displayer
getDisplayFields() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
getDisplayName() - Method in class org.intermine.web.logic.config.FieldConfig
Get the label to display in the webapp for this field.
getDisplayName() - Method in class org.intermine.web.logic.config.Type
 
getDisplayName() - Method in class org.intermine.web.logic.results.ReportObjectField
Get the label to display in the webapp for this field.
getDisplaySummary(PathQuery) - Static method in class org.intermine.web.logic.querybuilder.QueryBuilderSummaryHelper
Create summary information of the paths currently in a query and their constraints for display in the QueryBuilder summary section.
getDocument() - Method in class org.intermine.api.lucene.KeywordSearchHit
document
getDoesntContainOptions() - Method in class org.intermine.api.query.range.AbstractHelper
By default the DOES NOT CONTAINS options are negation of the CONTAINS options.
getDoesntOverlapOptions() - Method in class org.intermine.api.query.range.AbstractHelper
By default the DOES NOT OVERLAP options are negation of the OVERLAPS options.
getDoGzip() - Method in class org.intermine.web.struts.TableExportForm
Get whether the output should be GZIPped.
getDomain() - Method in class org.intermine.api.beans.PartnerLink
 
getDomain() - Method in class org.intermine.api.mines.ObjectRequest
 
getDomain() - Method in class org.intermine.webservice.server.jbrowse.Command
 
getDomainLabel() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
Get the domainLabel
getDoneAlready() - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Returns the doneAlready Set, for logging purposes
getDoNotTruncate() - Method in class org.intermine.web.logic.config.FieldConfig
Return the value of the doNotTruncate flag.
getDoNotTruncate() - Method in class org.intermine.web.logic.results.ReportObjectField
 
getDouble(String) - Method in class org.intermine.webservice.client.results.Item
Get a property known to be a double.
getDriver() - Method in class org.intermine.sql.Database
Gets the driver this Database
getECNumbers() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
geteditable() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
getEditableConstraints(String) - Method in class org.intermine.template.TemplateQuery
For a path with editable constraints, get all the editable constraints as a List, or the empty list if there are no editable constraints on that path.
getEditableConstraints() - Method in class org.intermine.template.TemplateQuery
Returns the list of all editable constraints.
getEditablePaths() - Method in class org.intermine.template.TemplateQuery
Get the paths of all editable constraints in this template.
getEditingConstraintCode() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Get the constraint that is being edited or null if creating a new constraint.
getEditingView(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the view list that the user is currently editing.
getEFactors(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return the rows needed for the experimental factors.
getEffectiveOrderBy() - Method in class org.intermine.objectstore.query.Query
Gets the effective ORDER BY clause of this Query, such as may be used to create SQL.
getEffectiveView() - Method in class org.intermine.webservice.server.core.TableRowIterator
 
getElementClassDescriptors() - Method in class org.intermine.pathquery.Path
Return a List of the ClassDescriptor objects for each element of the path.
getElementId() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
Return the table identifier if isTable==true.
getElements() - Method in class org.intermine.pathquery.Path
Return a list of field names, one per path element (except for the first, which is a class).
getElementsContainingField(String, String) - Method in class org.intermine.pathquery.Path
Return the indexes of elements containing the field given in input
getElementType() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the collection element type of the field.
getElementType(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the element type of a collection given the field name.
getElementType(String) - Method in interface org.intermine.model.InterMineFastPathObject
Returns the element type of a collection by name.
getElementType(String) - Method in interface org.intermine.model.InterMineObject
Returns the element type of a collection by name.
getElementType(String) - Method in class org.intermine.objectstore.proxy.ProxyReference
Returns the element type of a collection by name.
getEmail() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
 
getEmail() - Method in class org.intermine.webservice.server.JWTVerifier.Verification
 
getEmailAddress() - Method in class org.intermine.api.profile.Profile
Get this user's preferred email address.
getEmailer(Properties) - Static method in class org.intermine.web.context.EmailerFactory
 
getEncodedUrl() - Method in interface org.intermine.webservice.client.core.Request
 
getEncodedUrl() - Method in class org.intermine.webservice.client.core.RequestImpl
 
getEnd() - Method in interface org.intermine.api.query.range.Range
 
getEnd() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the end field of this record.
getEnd() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
Get start value
getEnd() - Method in class org.intermine.bio.web.model.GenomicRegion
 
getEnd() - Method in class org.intermine.objectstore.query.OverlapRange
Returns the right parameter.
getEnd() - Method in class org.intermine.webservice.server.core.Page
 
getEnd() - Method in class org.intermine.webservice.server.jbrowse.Segment
 
getEndClassDescriptor() - Method in class org.intermine.pathquery.Path
If the last element in the path is a reference or collection return the ClassDescriptor that the reference or collection references.
getEndClassName() - Method in class org.intermine.web.logic.query.DisplayConstraint
 
getEndFieldDescriptor() - Method in class org.intermine.pathquery.Path
Return the FieldDescriptor of the last element in the path or null if the path has just one element.
getEndRow() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the index of the last row of this page
getEndType() - Method in class org.intermine.pathquery.Path
Return the type of the last element in the path, regardless of whether it is an attribute or a class.
getEnrich() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
The enrich property is the path to the value that should be enriched.
getEnrichIdentifier() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getEnrichmentWidgets() - Method in class org.intermine.webservice.client.services.WidgetService
 
getEnsemblIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a Ensembl gene id resolver
getEnsemblIdResolver(boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a Ensembl gene resolver
getEnsemblPrefix() - Method in class org.intermine.bio.util.OrganismData
 
getEof() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Get the equivalent object fetcher.
getEquivalentObjects(InterMineObject, Source) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Returns a Set of objects from the idMap or database that are equivalent to the given object, according to the primary keys defined by the given Source.
getEquivalentsFor(List<ResultsRow<Object>>) - Method in class org.intermine.dataloader.BatchingFetcher
Fetches the equivalent object information for a whole batch of objects.
getEquivalentsForObjects(List<FastPathObject>) - Method in class org.intermine.dataloader.BatchingFetcher
Fetches the equivalent object information for a whole batch of objects.
getError() - Method in interface org.intermine.api.idresolution.Job
 
getError() - Method in class org.intermine.api.idresolution.ResolutionJob
 
getError() - Method in class org.intermine.api.idresolution.UpgradeJob
 
getError() - Method in class org.intermine.webservice.server.output.Output
Gets the error message.
getError() - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
 
getErrorCorrection() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
which method of errorcorrection the user chose.
getErrorCorrection() - Method in class org.intermine.web.struts.WidgetForm
 
getErrorElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
getErrorElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
 
getErrorOnInitialiser(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Gets the blocking error codes from the servlet context.
getErrors() - Method in class org.intermine.webservice.server.query.result.XMLValidator
Returns errors occurred during parsing xml.
getErrors() - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler
Returns errors occurred during parsing xml.
getErrorsAndWarnings() - Method in class org.intermine.webservice.server.query.result.XMLValidator
Returns errors and warning occurred during parsing xml.
getEscapeXml() - Method in class org.intermine.web.logic.config.FieldConfig
Return the value of the escapeXml flag.
getEscapeXml() - Method in class org.intermine.web.logic.results.ReportObjectField
 
getEstimatedRows() - Method in class org.intermine.sql.query.ExplainResult
Returns the best current estimate for the number of rows for this query.
getEstimatedSize() - Method in class org.intermine.api.results.WebResults
Get the estimated number of rows of this table
getEstimatedSize() - Method in interface org.intermine.api.results.WebTable
Get the estimated number of rows of this table
getEstimatedSize() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the (possibly estimated) number of resultElementRows of this table
getEvaluables() - Method in class org.intermine.objectstore.query.MultipleInBagConstraint
Returns the evaluables that this object was constructed with.
getEvent() - Method in class org.intermine.api.tracker.track.ListTrack
Return the type of event to track (creation or list execution )
getEventSetDescriptors() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getEventSetDescriptors() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getExactSize() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the exact number of resultElementRows of this table
getException() - Method in class org.intermine.api.lucene.InterMineObjectFetcher
Get the error that occurred during processing, if any.
getExcludeList() - Method in class org.intermine.task.ConverterTask
Return the list set by setExcludeList().
getExecutor() - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary
 
getExistingBagName() - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Gets the value of existingBagName
getExistingBagName() - Method in class org.intermine.web.struts.SaveBagForm
Gets the value of existingBagName
getExistingLoops() - Method in class org.intermine.pathquery.PathQuery
Returns the set of loop constraint descriptive strings, for the purpose of checking for uniqueness.
getExons() - Method in class org.intermine.bio.web.model.GeneModel
Get the exons if present.
getExperimentProperties(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return the rows needed for submission from the experiment_prop table.
getExperimentTitles(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return the rows needed for experiment from the experiment_prop table.
getExpiry() - Method in class org.intermine.webservice.server.user.DeletionToken
 
getExplain() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
Returns the ExplainResult of this Candidate, fetching the data if not already present.
getExplainResult(Query) - Method in class org.intermine.sql.precompute.BestQueryExplainer
Internal method that creates an ExplainResult.
getExplainResult(String) - Method in class org.intermine.sql.precompute.BestQueryExplainer
Internal method that creates an ExplainResult.
getExplainResult(Query) - Method in class org.intermine.sql.precompute.BestQueryExplainerVerbose
Internal method that creates an ExplainResult.
getExplainResult(String) - Method in class org.intermine.sql.precompute.BestQueryExplainerVerbose
Internal method that creates an ExplainResult.
getExplainText() - Method in class org.intermine.sql.query.PostgresExplainResult
Returns the text of the explain result, in human readable form.
getExportClassPaths(PagedTable) - Method in class org.intermine.bio.web.export.BEDHttpExporter
 
getExportClassPaths(PagedTable) - Method in class org.intermine.bio.web.export.GFF3HttpExporter
 
getExportClassPaths(PathQuery) - Static method in class org.intermine.bio.web.logic.SequenceFeatureExportUtil
From the view elements of a PathQuery, return a List of the Paths that this exporter will use to find sequences to export.
getExportClassPaths(PagedTable) - Static method in class org.intermine.bio.web.struts.GalaxyExportOptionsController
From the columns of the PagedTable, return a List of the Paths that this exporter will use to find sequences to export.
getExportClassPaths(PagedTable) - Method in class org.intermine.model.testmodel.web.EmployeeExporter
For EmployeeExporter we always return an empty list because all columns and classes are equal for this exporter.
getExporter(PathQuery) - Method in class org.intermine.bio.webservice.AbstractRegionExportService
 
getExporter(PathQuery) - Method in class org.intermine.bio.webservice.BEDQueryService
 
getExporter(PathQuery) - Method in class org.intermine.bio.webservice.BioQueryService
 
getExporter(PathQuery) - Method in class org.intermine.bio.webservice.FastaQueryService
 
getExporter(PathQuery) - Method in class org.intermine.bio.webservice.GAFQueryService
 
getExporter(PathQuery) - Method in class org.intermine.bio.webservice.GenomicRegionBedService
 
getExporter(PathQuery) - Method in class org.intermine.bio.webservice.GenomicRegionFastaService
 
getExporter(PathQuery) - Method in class org.intermine.bio.webservice.GenomicRegionGFF3Service
 
getExporter(PathQuery) - Method in class org.intermine.bio.webservice.GFFQueryService
 
getExporter(OutputStream, String, List<String>) - Method in class org.intermine.web.logic.export.http.CSVHttpExporter
Do the export.
getExporter(OutputStream, String, List<String>) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter
Do the export.
getExporter(OutputStream, String, List<String>) - Method in class org.intermine.web.logic.export.http.TabHttpExporter
Do the export.
getExporter(String) - Method in class org.intermine.web.logic.export.http.TableExporterFactory
Return the exporter class for the given id.
getExportFeaturesQuery(Set<Integer>, String, Set<String>, List<String>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
A flexiable way of setting query fields.
getExportField() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
getExportQuery(List<String>) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr
 
getExportResults(String[]) - Method in class org.intermine.web.logic.widget.EnrichmentWidget
 
getExportResults(String[]) - Method in class org.intermine.web.logic.widget.GraphWidget
getExportResults(String[]) - Method in class org.intermine.web.logic.widget.HTMLWidget
 
getExportResults(String[]) - Method in class org.intermine.web.logic.widget.TableWidget
getExportResults(String[]) - Method in class org.intermine.web.logic.widget.TableWidgetLdr
 
getExportResults(String[]) - Method in class org.intermine.web.logic.widget.Widget
 
getExporttype() - Method in class org.intermine.web.struts.WidgetForm
 
getExtendedEnd() - Method in class org.intermine.bio.web.model.GenomicRegion
 
getExtendedRegion() - Method in class org.intermine.bio.web.model.GenomicRegion
 
getExtendedRegionSize() - Method in class org.intermine.bio.web.model.GenomicRegion
 
getExtendedRegionSize() - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint
 
getExtendedStart() - Method in class org.intermine.bio.web.model.GenomicRegion
 
getExtension() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
 
getExtension() - Method in class org.intermine.webservice.server.query.CodeService
 
getExtension() - Method in class org.intermine.webservice.server.WebService
 
getExternalLink() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getExternalLink() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
getExternalLink() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
getExternalLinkLabel() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
getExtra() - Method in class org.intermine.api.profile.BagValue
 
getExtraAttribute() - Method in class org.intermine.web.logic.widget.PopulationInfo
 
getExtraAttribute() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
getExtraAttributes(ObjectStore, InterMineBag) - Method in class org.intermine.bio.web.widget.BioWidgetUtil
Get the extra attributes needed for the DataSetLoader
getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig
 
getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
Do-nothing implementation of superclass method
getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getExtraAttributes(ObjectStore, InterMineBag) - Method in interface org.intermine.web.logic.widget.WidgetHelper
Get the extra attributes needed for the DataSetLoader
getExtraConnectFieldPath() - Method in class org.intermine.web.logic.query.DisplayConstraint
 
getExtraConstraintClassName() - Method in class org.intermine.api.bag.BagQueryConfig
Return the class name that was passed to the constructor.
getExtraConstraintClassName() - Method in class org.intermine.web.logic.query.DisplayConstraint
If a LOOKUP constraint and an extra value constraint is available return the classname of the extra constraint so it can be displayed.
getExtraConstraintValues() - Method in class org.intermine.web.logic.query.DisplayConstraint
If a LOOKUP constraint and an extra constraint is available for this path, return a list of the possible values for populating a dropdown.
getExtraCorrectionCoefficient() - Method in interface org.intermine.web.logic.widget.EnrichmentOptions
 
getExtraCorrectionCoefficient() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
 
getExtraCorrectionCoefficient() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
getExtraFeatureConstraint() - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Return an extra constraint to be used when querying the feature table.
getExtraFeatureConstraint() - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Return an extra constraint to be used when querying the feature table.
getExtraFeatureConstraint() - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return an extra constraint to be used when querying the feature table.
getExtraFieldValue() - Method in class org.intermine.web.struts.BagUploadConfirmForm
Set the extra field value - the optional constraint on the bag upload page
getExtraFieldValue() - Method in class org.intermine.web.struts.BuildBagForm
Get the value to use when creating an extra constraint on a BagQuery, configured in BagQueryConfig.
getExtraFieldValue() - Method in class org.intermine.web.struts.ModifyBagDetailsForm
 
getExtraParams() - Method in class org.intermine.web.struts.TableExportForm
Extra parameters map for use by sub classes.
getExtraValue() - Method in interface org.intermine.api.idresolution.JobInput
 
getExtraValue(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint
A static method for getting the extra-value if there is one, or null if there is none to be got.
getExtraValue() - Method in class org.intermine.pathquery.PathConstraintLookup
Returns the extra value for this constraint.
getExtraValue() - Method in class org.intermine.template.TemplateValue
 
getExtraValue() - Method in class org.intermine.web.logic.bag.WebJobInput
 
getExtraValue() - Method in class org.intermine.web.logic.template.ConstraintInput
Returns extra value.
getExtraValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of extraValue
getExtraValue() - Method in class org.intermine.webservice.client.template.TemplateParameter
 
getExtraValue() - Method in class org.intermine.webservice.server.lists.ListInput
 
getExtraValue() - Method in class org.intermine.webservice.server.lists.ListsServiceInput
 
getExtraValueFieldClass() - Method in class org.intermine.web.logic.query.DisplayConstraint
 
getExtraValues() - Method in class org.intermine.web.struts.TemplateForm
Get the extra values
getExtraValues(String) - Method in class org.intermine.web.struts.TemplateForm
Get an extra value
getFacets() - Static method in class org.intermine.api.lucene.KeywordSearch
get list of facet fields and names
getFacets() - Method in class org.intermine.api.lucene.ResultsWithFacets
 
getFactory() - Static method in class org.intermine.bio.util.ClobAccessReverseComplement
Returns a ClobAccessSubclassFactory object that will access the constructor of this class quickly, in order to avoid using reflection for every clob.
getFactory() - Method in class org.intermine.webservice.client.core.Service
Get the ServiceFactory this service was constructed with.
getFastList(String, String, int) - Method in class org.intermine.web.autocompletion.AutoCompleter
Returns n search results
getFeature() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Return the feature Item set by setFeature()
getFeature() - Method in class org.intermine.bio.dataconversion.UniprotEntry
used to get the feature to store.
getFeatureAndSOInfo(InterMineAPI, Map<String, String>, int) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner
Query the information of all feature types and their according so terms.
getFeatureCds() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
Returns an unmodifiable set of the classdescriptors corresponding to the feature types in this query.
getFeatureClasses() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
 
getFeatureCVTermResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return the interesting rows from the feature_cvterm/cvterm table.
getFeatureIdQuery() - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return an SQL query that finds the feature_ids of all rows from the feature table that we need to process.
getFeatureLocResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return the interesting rows from the featureloc table.
getFeatureMap() - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Fetch the populated map of chado feature id to FeatureData objects.
getFeaturePropResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return the interesting rows from the featureprop table.
getFeatureRelationshipResultSet(Connection, boolean) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return the interesting rows from the feature_relationship table.
getFeatures() - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Get a list of the chado/so types of the LocatedSequenceFeatures we wish to load.
getFeatures() - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Get a list of the chado/so types of the LocatedSequenceFeatures we wish to load.
getFeatures() - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Get a list of the chado/so types of the SequenceFeatures we wish to load.
getFeatures() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getFeatures() - Method in class org.intermine.bio.dataconversion.WormBaseProcessor
Get a list of the chado/so types of the LocatedSequenceFeatures we wish to load.
getFeatureTableResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return the interesting rows from the features table.
getFeatureTypes() - Method in class org.intermine.bio.dataconversion.UniprotConfig
if NULL, all feature types will be loaded.
getFeatureTypes() - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint
 
getFeatureTypes() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
 
getFeatureTypeSetInAlphabeticalOrder(Set<String>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Get all feature types in a TresSet
getFeatureTypeToSOTermMap() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
 
getField() - Method in class org.intermine.api.lucene.KeywordSearchFacet
internal field name
getField() - Method in class org.intermine.api.lucene.KeywordSearchFacetData
get single/first field or null
getField() - Method in interface org.intermine.api.results.ResultCell
 
getField() - Method in class org.intermine.api.results.ResultElement
Get the field value
getField() - Method in class org.intermine.webservice.server.core.TableCell
 
getFieldConfig(WebConfig, FieldDescriptor) - Static method in class org.intermine.web.logic.config.FieldConfigHelper
Get a field config object for a particular descriptor.
getFieldConfig(WebConfig, ClassDescriptor, FieldDescriptor) - Static method in class org.intermine.web.logic.config.FieldConfigHelper
Get a field config object for a particular descriptor.
getFieldConfig(String) - Method in class org.intermine.web.logic.config.Type
Return a FieldConfig for a particular field if it has been specified, otherwise return null
getFieldConfig(String, String) - Method in class org.intermine.web.logic.config.WebConfig
Return the FieldConfig for a particular field of the specified field, or null if field not configured.
getFieldConfig() - Method in class org.intermine.web.logic.results.InlineTableResultElement
 
getFieldConfigMap() - Method in class org.intermine.web.logic.config.Type
Return a Map from FieldConfig.fieldName to FieldConfig objects.
getFieldConfigs() - Method in class org.intermine.web.logic.config.Type
Get the List of FieldConfig objects
getFieldConfigs(String) - Method in class org.intermine.web.logic.config.WebConfig
Return a FieldConfigs for a particular class or an empty list if no config is defined.
getFieldConfigs() - Method in class org.intermine.web.logic.results.ReportObject
Return a list of field configs
getFieldConfigs() - Method in class org.intermine.web.search.KeywordSearchResult
fieldConfigs
getFieldDescriptor() - Method in class org.intermine.pathquery.Node
 
getFieldDescriptor() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Return the last field descriptor (the last element) of the path.
getFieldDescriptor() - Method in class org.intermine.web.logic.results.InlineResultsTable
Get the fields descriptor this list represents.
getFieldDescriptorByName(String) - Method in class org.intermine.metadata.ClassDescriptor
Retrieve a FieldDescriptor by name.
getFieldDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets the FieldDescriptors for this class (but not superclasses).
getFieldDescriptorsForClass(Class<?>) - Method in class org.intermine.metadata.Model
Takes a Class, and generates a Map of all FieldDescriptors that are the class fields or any of its parents.
getFieldDisplayName(String) - Method in class org.intermine.web.logic.results.ReportObject
Return a string to display as the name of a field.
getFieldExporter() - Method in class org.intermine.web.logic.config.FieldConfig
Return the class name of the FieldExporter to use when this field is viewed.
getFieldExpr() - Method in class org.intermine.web.logic.config.FieldConfig
Return the JSTL expression for the object.
getFieldInfo(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns a FieldInfo object for the given class and field name.
getFieldInfos(Class<?>) - Static method in class org.intermine.metadata.TypeUtil
Returns the Map from field name to TypeUtil.FieldInfo objects for all the fields in a given class.
getFieldName() - Method in class org.intermine.bio.chado.config.CreateCollectionAction
Return the fieldName that was passed to the constructor.
getFieldName() - Method in class org.intermine.bio.chado.config.SetFieldConfigAction
Return the field name that was passed to the constructor.
getFieldName() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the name of the field.
getFieldName() - Method in class org.intermine.objectstore.query.QueryField
Returns the name of the field.
getFieldName() - Method in class org.intermine.objectstore.query.QueryForeignKey
Gets the fieldname of this QueryReference.
getFieldName() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Returns the name of the field.
getFieldName() - Method in class org.intermine.objectstore.query.QueryReference
Gets the fieldname of this QueryReference.
getFieldName() - Method in class org.intermine.pathquery.Node
Gets the value of fieldName
getFieldName(int) - Method in class org.intermine.web.autocompletion.LuceneObjectClass
return the fieldName at position index
getFieldName() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns the fieldname for this path.
getFieldNames() - Method in class org.intermine.api.lucene.InterMineObjectFetcher
get list of fields contained in the fetched documents
getFieldNames() - Method in class org.intermine.metadata.PrimaryKey
Return the Set of field names
getFieldNames() - Method in class org.intermine.web.autocompletion.LuceneObjectClass
getFieldNames
getFieldNumber() - Method in class org.intermine.objectstore.query.PathExpressionField
Returns the field number.
getFieldProxy(Object, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the value of a public or protected Field of an Object given by the field name without dereferencing any ProxyReference objects.
getFieldProxy(String) - Method in interface org.intermine.model.FastPathObject
Returns the value of a field without dereferencing any ProxyReference objects.
getFieldProxy(String) - Method in class org.intermine.objectstore.proxy.ProxyReference
Returns the value of a field without dereferencing any ProxyReference objects.
getFields() - Method in class org.intermine.api.lucene.KeywordSearchFacetData
array of field names, only used for path right now
getFields() - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary
 
getFieldToAlias(FromElement) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getFieldType(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the type of a field given the field name.
getFieldType(String) - Method in interface org.intermine.model.FastPathObject
Returns the type of a field by name.
getFieldType(String) - Method in class org.intermine.objectstore.proxy.ProxyReference
Returns the type of a field by name.
getFieldValue(Object, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the value of a public or protected Field of an Object given the field name
getFieldValue(String) - Method in interface org.intermine.model.FastPathObject
Returns the value of a field by name.
getFieldValue(String) - Method in class org.intermine.objectstore.proxy.ProxyReference
Returns the value of a field by name.
getFieldValue(String) - Method in class org.intermine.web.logic.results.ReportObject
Get field value for a field name (expression)
getFieldValues(String, String) - Method in class org.intermine.objectstore.ObjectStoreSummary
Get a list of the possible values (as Strings) for a given field in a given class.
getFieldValues() - Method in class org.intermine.web.search.KeywordSearchResult
values of all fields
getFieldValues(ObjectStore, ObjectStoreSummary, String, String) - Static method in class org.intermine.web.struts.BagBuildController
Return a list of the possible field values for the given class/field name combination.
getFileName() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
Returns the filename that should be associated with this query.
getFilename(String, String) - Static method in class org.intermine.metadata.Util
Given a key and model name, return filename for reading/writing.
getFilename(String, String) - Static method in class org.intermine.modelproduction.MetadataManager
Given a key and model name, return filename for reading/writing.
getFilter() - Method in interface org.intermine.web.logic.widget.WidgetOptions
 
getFilter() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
filter values get used in the query to constrain the results in some way, and they can be changed by the user.
getFilter() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
getFilterLabel() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getFilterLabel() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
the label for the filter.
getFilters() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getFilters() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
filter values get used in the query to constrain the results in some way, and they can be changed by the user.
getFilters() - Method in class org.intermine.webservice.client.widget.Widget
 
getFiltersValues(ObjectStore, InterMineBag) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getFilterWebSearchables(HttpServletRequest, String, String, String) - Static method in class org.intermine.web.struts.WebSearchableListController
Get all the WebSearchables in the given scope and of the given type.
getFinalItems() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Return items that need extra processing that can only be done after all other GFF features have been read.
getFirstAlias() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the first value of the Alias field from the attributes of this record.
getFirstColumnForClass(PagedTable, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper
Find the first column index for the specified class or a subclass in the page table (may be a parent class of a field being displayed).
getFirstOrderByHasNoNulls() - Method in class org.intermine.sql.precompute.PrecomputedTable
Returns true if the first element of the ORDER BY clause is a column that contains no nulls.
getFirstSelectedFields(ObjectStore, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return the fields for the first selected objects.
getFishIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a fish id resolver
getFishIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a fish id resolver
getFishIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a fish id resolver
getFivePrimeUTR() - Method in class org.intermine.bio.web.model.GeneModel
Get the fivePrimeUTR if present.
getFixedOps() - Method in class org.intermine.web.logic.query.DisplayConstraint
If a dropdown is available for a constraint fewer operations are possible, return the list of operations.
getFlatSelect() - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
Converts a SELECT list from a normal query into a representation of the columns returned in this converted list.
getFlattenedResults() - Method in class org.intermine.web.logic.widget.TableWidget
Get the flattened results
getFlattenedResults() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
get the flattened results
getFloat(String) - Method in class org.intermine.webservice.client.results.Item
Get a property known to be an float.
getFlyBaseMiscCV(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Get ChadoCV object representing the FlyBase misc cv.
getFlyBaseSequenceOntologyCV(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Get ChadoCV object representing SO from FlyBase.
getFlyIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a fly id resolver
getFlyIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a fly id resolver
getFlyIdResolver(Set<String>) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a fly id resolver
getFlyIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a fly id resolver
getFlyIdResolver(Set<String>, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a fly id resolver
getFooter() - Static method in class org.intermine.xml.full.FullRenderer
Return the Full XML file footer
getFormat() - Method in enum org.intermine.api.mines.ContentType
 
getFormat() - Method in class org.intermine.web.struts.CSVExportForm
Return the format field ("csv", "tab", ...)
getFormat() - Method in class org.intermine.webservice.server.WebService
Returns required output format.
getFormatted() - Method in class org.intermine.web.logic.results.ReportObject.TitleValue
Get the formatted version, with e.g. italics tags.
getFormattedClassName() - Method in class org.intermine.web.logic.config.Type
 
getFormattedClassName(String) - Static method in class org.intermine.web.logic.config.Type
 
getFormattedName() - Method in class org.intermine.web.logic.config.FieldConfig
 
getFormattedName(String) - Static method in class org.intermine.web.logic.config.FieldConfig
 
getFormattedTrack() - Method in class org.intermine.api.tracker.track.KeySearchTrack
 
getFormattedTrack() - Method in class org.intermine.api.tracker.track.ListTrack
Return the track formatted into an array of String to be saved in the database
getFormattedTrack() - Method in class org.intermine.api.tracker.track.LoginTrack
Return the track formatted into an array of String to be saved in the database
getFormattedTrack() - Method in class org.intermine.api.tracker.track.QueryTrack
 
getFormattedTrack() - Method in class org.intermine.api.tracker.track.TemplateTrack
Return the track formatted into an array of String to be saved in the database
getFormattedTrack() - Method in interface org.intermine.api.tracker.track.Track
Return the track formatted into an array of String to be saved in the database
getFormatter() - Method in class org.intermine.bio.webservice.AbstractRegionExportService
 
getFormatter() - Static method in class org.intermine.webservice.server.core.ISO8601DateFormat
 
getFormFile() - Method in class org.intermine.web.struts.BuildBagForm
Get the FormFile.
getFormFile() - Method in class org.intermine.web.struts.ImportXMLForm
Get the FormFile.
getFragmentFromURI(String) - Static method in class org.intermine.util.XmlUtil
Return the fragment portion of a URI string (i.e. everything after a #).
getFriendlyDesc(Object) - Static method in class org.intermine.util.DynamicUtil
Creates a friendly description of an object - that is, the class and the ID (if it has one).
getFriendlyMineLinks(String, String, String) - Static method in class org.intermine.dwr.AjaxServices
used on REPORT page For a gene, generate links to other intermines.
getFriendlyMines() - Method in class org.intermine.api.mines.FriendlyMineManager
Return a list of Mines listed in config.
getFriendlyName(Class<?>) - Static method in class org.intermine.metadata.Util
Creates a friendly name for a given class.
getFriendlyName() - Method in class org.intermine.pathquery.Node
Gets a friendly name for display on the web site.
getFriendlyName() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns the last element of the path.
getFrom() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getFrom() - Method in class org.intermine.objectstore.query.Query
Returns all FromElements in the FROM clause
getFrom() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the additional FROM list.
getFrom() - Method in class org.intermine.sql.query.Query
Gets the Set of from tables for this query.
getFromElement() - Method in class org.intermine.objectstore.query.QueryField
Gets the FromElement of which the field is a member
getFrontcolor() - Method in class org.intermine.api.mines.LocalMine
 
getFrontcolor() - Method in interface org.intermine.api.mines.Mine
 
getFrontcolor() - Method in class org.intermine.api.mines.RemoteMine
 
getFullName(String) - Static method in class org.intermine.webservice.server.CodeTranslator
Returns corresponding fullName of translated operation.
getFullRegionInfo() - Method in class org.intermine.bio.web.model.GenomicRegion
 
getGap() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the first value of the Gap field from the attributes of this record.
getGene() - Method in class org.intermine.bio.web.model.GeneModel
The parent gene for this gene model.
getGeneDesignation() - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
Where to get the gene identifier from. e.g. in WormBase, it's the gene ID.
getGeneDesignation(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig
A string value, e.g.
getGeneDesignation(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
getGeneIdentifierFields(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig
 
getGeneInfoRecords() - Method in class org.intermine.bio.dataconversion.NcbiGeneInfoParser
Return information read from the file, for each taxon id there is one GeneInfoRecord per row in the file.
getGeneModelIds(InterMineObject, Model) - Static method in class org.intermine.bio.web.model.GeneModelCache
Look up the gene models for a given gene or gene model component and return the ids of all objects involved.
getGeneModelOrganismSettings(String, ObjectStore) - Static method in class org.intermine.bio.web.model.GeneModelCache
 
getGeneModels(InterMineObject, Model) - Static method in class org.intermine.bio.web.model.GeneModelCache
Fetch a list of gene models for a gene.
getGeneNames() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getGeneratedPathDescription(String) - Method in class org.intermine.pathquery.PathQuery
Returns the path description for the given path.
getGenomeBuild() - Method in class org.intermine.bio.web.model.OrganismInfo
 
getGenomeBuildbyOrgansimAbbreviation(String) - Static method in class org.intermine.bio.web.logic.OrganismGenomeBuildLookup
Get genome build by organism short name such as "D. melanogaster"
getGenomeBuildByOrgansimCollection(Collection<String>) - Static method in class org.intermine.bio.web.logic.OrganismGenomeBuildLookup
Get genome build by a collection of ids
getGenomeBuildbyOrgansimFullName(String) - Static method in class org.intermine.bio.web.logic.OrganismGenomeBuildLookup
Get genome build by organism full name such as "Drosophila melanogaster"
getGenomeBuildbyOrgansimId(String) - Static method in class org.intermine.bio.web.logic.OrganismGenomeBuildLookup
Get genome build by any id
getGenomeBuildbyOrgansimTaxon(Integer) - Static method in class org.intermine.bio.web.logic.OrganismGenomeBuildLookup
Get genome build by organism taxon such as 7227
getGenomicRegionExtendedSizeConstraint(String, Map<GenomicRegionSearchConstraint, String>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Get flanking size for GenomicRegionSearchAjaxAction use.
getGenomicRegionList() - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint
 
getGenomicRegionOrganismConstraint(String, Map<GenomicRegionSearchConstraint, String>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Get organism for GenomicRegionSearchAjaxAction use.
getGenomicRegionOverlapFeaturesAsSet(String, Map<GenomicRegion, List<List<String>>>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Get a set of ids of a span's overlap features. for GenomicRegionSearchAjaxAction use.
getGenomicRegionOverlapFeaturesAsString(String, Map<GenomicRegion, List<List<String>>>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Get a comma separated string of a span's overlap features. for GenomicRegionSearchAjaxAction use.
getGenomicRegionOverlapFeaturesByType(String, Map<GenomicRegion, List<List<String>>>, String) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Get a set of ids of a span's overlap features by given feature type. for GenomicRegionSearchAjaxAction use.
getGenomicRegions() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
 
getGenomicRegionSearchService(HttpServletRequest) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchUtil
Generate GenomicRegionSearchService object by using Java reflection
getGenus() - Method in class org.intermine.bio.util.OrganismData
Get the genus of this organism.
getGetter() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the getter Method.
getGetter(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the Method object that is the getter for the field name.
getGetters(Class<?>) - Static method in class org.intermine.metadata.TypeUtil
Gets the getter methods for the bean properties of a class
getGlobalBag(String) - Method in class org.intermine.api.bag.BagManager
Fetch a global bag by name.
getGlobalBags() - Method in class org.intermine.api.bag.BagManager
Fetch globally available bags - superuser public bags that are available to everyone.
getGlobalBagsContainingId(Integer) - Method in class org.intermine.api.bag.BagManager
Fetch global bags that contain the given id.
getGlobalBagsWithTags(List<String>) - Method in class org.intermine.api.bag.BagManager
Fetch globally available bags - superuser public bags that are available to everyone with a particular tag assigned to them
getGlobalSearchRepositories() - Static method in class org.intermine.api.search.SearchRepository
Get the search repositories registered as global repositories.
getGlobalSearchRepository(Profile) - Static method in class org.intermine.api.search.SearchRepository
Get the search repository registered as global repositories for the user specified in input.
getGlobalSearchRepository(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the SearchRepository for global (public) objects.
getGlobalTemplate(String) - Method in class org.intermine.api.template.TemplateManager
Fetch a global template by name.
getGlobalTemplates() - Method in class org.intermine.api.template.TemplateManager
Return a map from template name to template query containing superuser templates that are tagged as public.
getGlobalTemplates(boolean) - Method in class org.intermine.api.template.TemplateManager
Return a map from template name to template query containing superuser templates that are tagged as public.
getGOEvidence(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getGoIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a GO id resolver
getGoIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a GO id resolver
getGOTerms() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getGraphType() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
Get the type of this graph, e.g.
getGroupBy() - Method in class org.intermine.objectstore.query.Query
Gets the GROUP BY clause of this Query
getGroupBy() - Method in class org.intermine.sql.query.Query
Gets the Set of fields in the GROUP BY clause of this query.
getGroupedConstraintLogic() - Method in class org.intermine.pathquery.PathQuery
Returns a List of logic Strings according to the different outer join sections of the query.
getHasAvailableBags() - Method in class org.intermine.web.logic.query.MetadataNode
Returns true if there are any available bags for the type of this path.
getHasCDSs() - Method in class org.intermine.bio.web.model.GeneModelSettings
 
getHasClassKeys() - Method in class org.intermine.web.logic.query.MetadataNode
Returns true if the type of this path has class keys configured.
getHasDisplayer() - Method in class org.intermine.web.logic.results.InlineTableResultElement
 
getHasExons() - Method in class org.intermine.bio.web.model.GeneModelSettings
 
getHasFivePrimeUTRs() - Method in class org.intermine.bio.web.model.GeneModelSettings
 
getHasGenes() - Method in class org.intermine.bio.web.model.GeneModelSettings
 
getHasHeaderInlineLists() - Method in class org.intermine.web.logic.results.ReportObject
Used from JSP
getHasIntrons() - Method in class org.intermine.bio.web.model.GeneModelSettings
 
getHasMoreThanOneType() - Method in class org.intermine.web.logic.results.InlineResultsTable
 
getHasNormalInlineLists() - Method in class org.intermine.web.logic.results.ReportObject
Used from JSP
getHasPossibleLoops() - Method in class org.intermine.web.logic.query.MetadataNode
Returns true if this path in the query has possible loop constraints that are not already in the query.
getHasResults() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
getHasResults() - Method in class org.intermine.web.logic.widget.GraphWidget
getHasResults() - Method in class org.intermine.web.logic.widget.HTMLWidget
 
getHasResults() - Method in class org.intermine.web.logic.widget.TableWidget
getHasResults() - Method in class org.intermine.web.logic.widget.Widget
 
getHasSubclasses() - Method in class org.intermine.web.logic.query.MetadataNode
Returns true if the original type has subclasses in the model.
getHasThreePrimeUTRs() - Method in class org.intermine.bio.web.model.GeneModelSettings
 
getHasTranscripts() - Method in class org.intermine.bio.web.model.GeneModelSettings
 
getHaving() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getHaving() - Method in class org.intermine.sql.query.Query
Gets the set of constraints forming the HAVING clause of this query.
getHavingBuffer() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getHeadAttributes() - Method in class org.intermine.api.template.ApiTemplate
 
getHeadAttributes() - Method in class org.intermine.pathquery.PathQuery
 
getHeadAttributes() - Method in class org.intermine.template.TemplateQuery
 
getHeader(String) - Method in interface org.intermine.webservice.client.core.Request
Returns the header value.
getHeader(String) - Method in class org.intermine.webservice.client.core.RequestImpl
Returns the header value.
getHeader() - Static method in class org.intermine.xml.full.FullRenderer
Return the Full XML file header
getHeaderAttributes() - Method in class org.intermine.bio.webservice.GenomicRegionSearchService
Gets the header attributes on the output object.
getHeaderAttributes() - Method in class org.intermine.webservice.server.clob.SequenceService
Why is the results key "features", pray?
getHeaderAttributes() - Method in class org.intermine.webservice.server.core.JSONService
Get the header attributes to apply to the formatter.
getHeaderAttributes() - Method in class org.intermine.webservice.server.jbrowse.Endpoint
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListMakerService
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationDetailsService
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListTagService
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListUploadService
Gets the header attributes on the output object.
getHeaderAttributes() - Method in class org.intermine.webservice.server.output.Output
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.path.PossibleValuesService
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.search.QuickSearch
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.user.NewUserService
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.VersionService
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.widget.AvailableWidgetsService
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.widget.WidgetService
 
getHeaderConfigLink() - Method in class org.intermine.web.logic.config.Type
 
getHeaderConfigTitle() - Method in class org.intermine.web.logic.config.Type
 
getHeaderInlineLists() - Method in class org.intermine.web.logic.results.ReportObject
 
getHeaderLink() - Method in class org.intermine.web.logic.results.ReportObject
 
getHeaders() - Method in interface org.intermine.webservice.client.core.Request
Returns request headers.
getHeaders() - Method in class org.intermine.webservice.client.core.RequestImpl
Returns request headers.
getHeadResources(String, Map<String, String>) - Static method in class org.intermine.web.logic.WebUtil
Returns the resources for a particular section of the head element.
getHelper(Class<?>) - Static method in class org.intermine.api.query.MainHelper.RangeConfig
 
getHelpMessage() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return a help message to display alongside the constraint, this will examine the constraint type and generate and appropriate message, e.g. list the key fields for LOOKUP constraints and explain the use of wildcards.
getHelpMessage(DisplayConstraint) - Static method in class org.intermine.web.logic.query.DisplayConstraintHelpMessages
Generate a context sensitive help message for a constraint.
getHelpPage(HttpServletRequest) - Static method in class org.intermine.web.logic.WebUtil
Look at the current webapp page and subtab and return the help page and tab.
getHgncIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a HGNC human gene id resolver
getHgncIdResolver(boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a HGNC human gene resolver
getHide() - Method in class org.intermine.web.logic.config.FieldConfig
Return the value of the hide flag.
getHighlight() - Method in class org.intermine.web.struts.WidgetForm
 
getHighlightedLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Returns html formatted link in which are highlighted parameters that are to be replaced. * @see #getLink(String, TemplateQuery)
getHintCount(String) - Method in class org.intermine.web.logic.results.WebState
Get the number of times a particular hint has been shown.
getHintForPage(String, WebState) - Method in class org.intermine.web.logic.help.HintManager
Fetch a hint for the given page or return null if there are no hints or all hints have been displayed the maximum number of times.
getHistory() - Method in class org.intermine.api.profile.Profile
Get the session query history.
getHits() - Method in class org.intermine.api.lucene.ResultsWithFacets
 
getHtmlHeadTitle() - Method in class org.intermine.web.logic.results.ReportObject
Fetch a header string to use as the page title.
getHtmlLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Generates TemplateResultService web service link.
getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.BadRequestException
 
getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.InternalErrorException
 
getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.NotImplementedException
 
getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.ResourceNotFoundException
 
getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.ServiceException
 
getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.ServiceForbiddenException
 
getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.ServiceUnavailableException
 
getHttpErrorCode() - Method in exception org.intermine.webservice.server.exceptions.ServiceException
 
getHumanIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a Human gene id resolver
getHumanIdResolver(boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a Human gene resolver
getHumanReadableText() - Method in class org.intermine.metadata.ClassDescriptor
Returns a String that contains a multi-line human-readable description of the ClassDescriptor.
getIcon(int) - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getIcon(int) - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getIconImage() - Method in class org.intermine.web.logic.aspects.Aspect
Get the icon Image.
getID() - Method in class org.intermine.api.mines.LocalMine
 
getId() - Method in interface org.intermine.api.results.ResultCell
 
getId() - Method in class org.intermine.api.results.ResultElement
Get the Id.
getId() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the first value of the Id field from the attributes of this record.
getId() - Method in class org.intermine.bio.ontology.OboTerm
Get the id of this term.
getId() - Method in class org.intermine.bio.ontology.OboTypeDefinition
 
getId() - Method in interface org.intermine.model.InterMineFastPathObject
Getter for the ID field - ensures that every object in the database has an ID.
getId() - Method in interface org.intermine.model.InterMineObject
Getter for the ID field - ensures that every object in the database has an ID.
getId() - Method in class org.intermine.objectstore.proxy.ProxyReference
Gets the ID value
getId() - Method in class org.intermine.web.logic.config.InlineListObject
 
getId() - Method in class org.intermine.web.logic.config.TableExportConfig
Return the id of this TableExportConfig.
getId() - Method in class org.intermine.web.logic.results.DisplayReference
Get the id of the object
getId() - Method in class org.intermine.web.logic.results.ReportObject
Get the id of this object
getId() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getId() - Method in class org.intermine.web.search.KeywordSearchResult
intermine ID
getId() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
 
getId() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Gets element id.
getId() - Method in class org.intermine.webservice.client.results.Item
Get the internal database id of the object.
getId() - Method in class org.intermine.webservice.server.core.TableCell
 
getIdentifier() - Method in class org.intermine.api.beans.ObjectDetails
 
getIdentifier() - Method in class org.intermine.api.mines.ObjectRequest
 
getIdentifier(Sequence) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
For the given BioJava Sequence object, return an identifier to be used when creating the corresponding BioEntity.
getIdentifier(Sequence) - Method in class org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask
For the given BioJava Sequence object, return an identifier to be used when creating the corresponding BioEntity.
getIdentifier(Sequence) - Method in class org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask
For the given BioJava Sequence object, return an identifier to be used when creating the corresponding BioEntity.
getIdentifier(Sequence) - Method in class org.intermine.bio.dataconversion.NCBIFastaLoaderTask
For the given BioJava Sequence object, return an identifier to be used when creating the corresponding BioEntity.
getIdentifier() - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
Used from JSP
getIdentifier() - Method in class org.intermine.xml.full.Item
Get the identifier of this item.
getIdentifierFields() - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
which fields in gene object we are setting, eg. primaryIdentifier or secondaryIdentifier
getIdentifierMethod(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
 
getIdentifierMethod(String, String) - Method in class org.intermine.bio.dataconversion.UniprotConfig
 
getIdentifierName() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
 
getIdentifierSource() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
Where we should get the identifier will either be an Xref database, e.g.
getIdentifierValue(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
 
getIdentifierValue(String, String) - Method in class org.intermine.bio.dataconversion.UniprotConfig
 
getIdentity() - Method in class org.intermine.webservice.server.JWTVerifier.Verification
 
getIdField() - Method in class org.intermine.sql.writebatch.TableBatch
Returns the idField.
getIdMap() - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Returns the IdMap used.
getIdResolver() - Method in class org.intermine.bio.dataconversion.DoNothingIdResolverFactory
 
getIdResolver(String) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
Return an IdResolver by taxon id, if not already built then create it.
getIdResolver(Set<String>) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
Return an IdResolver by a list of taxon id, if not already built then create it.
getIdResolver(String, boolean) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
Return an IdResolver by taxon id, if not already built then create it.
getIdResolver(Set<String>, boolean) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
Return an IdResolver by a list of taxon ids, if not already built then create it.
getIdResolver() - Method in class org.intermine.bio.dataconversion.IdResolverFactory
Return an IdResolver, if not already built then create it.
getIdResolver(boolean) - Method in class org.intermine.bio.dataconversion.IdResolverFactory
Return an IdResolver, if not already built then create it.
getIdResolver() - Method in class org.intermine.bio.dataconversion.MockIdResolverFactory
Create a MockIdResolver
getIdResolver() - Method in class org.intermine.bio.dataconversion.OntologyIdResolverFactory
Return an IdResolver, if not already built then create it.
getIdResolver(boolean) - Method in class org.intermine.bio.dataconversion.OntologyIdResolverFactory
Return an IdResolver, if not already built then create it.
getIdResolverByOrganism(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a Entrez Gene Id Resolver by given taxonId
getIdResolverByOrganism(Set<String>) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a Entrez Gene Id Resolver by given taxonId set
getIdResolverByTaxonId(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a Entrez Gene Id Resolver by given taxonId
getIdResolverByTaxonId(Set<String>, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a Entrez Gene Id Resolver by given taxonId set
getIdResolverForMOD() - Static method in class org.intermine.bio.dataconversion.IdResolverService
 
getIds() - Method in interface org.intermine.api.idresolution.JobInput
 
getIds() - Method in class org.intermine.bio.web.model.GeneModel
Return the ids of all objects represented in this gene model including the gene itself.
getIds() - Method in class org.intermine.objectstore.query.QueryClassBag
Returns the Set of object IDs present in the bag that correspond to the type specified.
getIds(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint
Get the ids for a constraint.
getIds() - Method in class org.intermine.pathquery.PathConstraintIds
Returns the id collection that the constraint is constraining to.
getIds() - Method in class org.intermine.web.logic.bag.WebJobInput
 
getIdsContained(Collection<Integer>) - Method in class org.intermine.api.profile.InterMineBag
Returns a List which contains the ids given in input and contained in this bag as Integer IDs.
getIdsToDelete() - Method in class org.intermine.sql.writebatch.TableBatch
Returns the delete set.
getIdsToInsert() - Method in class org.intermine.sql.writebatch.TableBatch
Returns the insert map.
getIdsToRemove(InterMineBag) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the IDs to remove.
getIdx() - Method in class org.intermine.bio.web.model.OrganismInfo
 
getIgnoredTaxonIds() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
used for testing
getImage() - Method in class org.intermine.web.logic.config.HeaderConfigLink
 
getImageName() - Method in class org.intermine.bio.web.XRef
 
getIMObjectForSequence(ObjectStore, Class, Sequence) - Static method in class org.intermine.bio.web.export.ResidueFieldExporter
Find the IntermineObject that references the given Sequence.
getImplementations() - Method in class org.intermine.xml.full.Item
Get the interfaces implemented by this item.
getImplementClassDescriptors(String) - Method in class org.intermine.xml.full.Item
Returns the ClassDescriptors for the given implementations.
getImplements(Object, Model) - Static method in class org.intermine.xml.full.ItemFactory
Get all interfaces that an object implements.
getIncludeHeaders() - Method in class org.intermine.web.struts.TableExportForm
Return the current value of the includeHeaders flag.
getIndelResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Return a result set containing pairs of chromosome_structure_variation (deletions) and transposable_element_insertion_site (insertions).
getIndentation() - Method in class org.intermine.pathquery.Node
Gets the value of indentation
getIndentation() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns the number of elements in the path, where a simple class is zero.
getIndentation() - Method in class org.intermine.web.logic.TreeNode
Get the indentation
getIndex() - Method in class org.intermine.api.results.Column
Gets the value of index
getIndex() - Method in class org.intermine.metadata.ConstraintOp
Get an index for this ConstraintOp TODO: expunge this horror.
getIndexSearch() - Method in class org.intermine.web.autocompletion.LuceneSearchEngine
returns the indexSearcher so we can use IndexSearcher.doc(int) to get a doc
getIndexWriter(boolean, String) - Method in class org.intermine.web.autocompletion.LuceneIndex
returns the index writer
getIndirectAlias() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getIndirectionTableName(CollectionDescriptor) - Static method in class org.intermine.sql.DatabaseUtil
Creates an indirection table name for a many-to-many collection descriptor
getIndirectionTableNames(ClassDescriptor) - Static method in class org.intermine.sql.DatabaseUtil
Given a ClassDescriptor find names of all related indirection tables.
getInfo() - Method in class org.intermine.api.results.WebResults
Return the ResultsInfo object from the underlying Results object.
getInfo() - Method in interface org.intermine.api.results.WebTable
Gets the underlying results object info
getInfo() - Method in interface org.intermine.objectstore.proxy.LazyCollection
Returns Returns the current best estimate of the characteristics of the LazyCollection
getInfo() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Returns Returns the current best estimate of the characteristics of the LazyCollection
getInfo() - Method in class org.intermine.objectstore.query.Results
Gets the best current estimate of the characteristics of the query.
getInfo() - Method in class org.intermine.objectstore.query.ResultsBatches
Gets the best current estimate of the characteristics of the query.
getInfoCache() - Method in class org.intermine.api.query.WebResultsExecutor
Returns the entire infoCache, which is an unmodifiable Map from PathQuery (by identity) to ResultsInfo.
getInitialExportPaths(PagedTable) - Method in class org.intermine.bio.web.export.BEDHttpExporter
The intial export path list is just the paths from the columns of the PagedTable.
getInitialExportPaths(PagedTable) - Method in class org.intermine.bio.web.export.GFF3HttpExporter
The intial export path list is just the paths from the columns of the PagedTable.
getInitialExportPaths(PagedTable) - Method in class org.intermine.bio.web.export.SequenceHttpExporter
The intial export path list is just the paths from the columns of the PagedTable with chromosomeLocation added (if appropriate) Return a list of the Paths to show the user as initial export columns or header contents.
getInitialExportPaths(PagedTable) - Method in class org.intermine.model.testmodel.web.EmployeeExporter
The intial export path list is just the paths from the columns of the PagedTable.
getInitialExportPaths(PagedTable) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter
The initial export path list is just the paths from the columns of the PagedTable.
getInitialExportPaths(PagedTable) - Method in interface org.intermine.web.logic.export.http.TableHttpExporter
Return a list of the Paths to show the user as initial export columns or header contents.
getInlineListConfig() - Method in class org.intermine.web.logic.config.Type
 
getInput() - Method in class org.intermine.api.idresolution.ResolutionJob
 
getInput() - Method in class org.intermine.bio.webservice.GenomicRegionSearchService
 
getInput() - Method in class org.intermine.webservice.server.lists.AbstractListService
 
getInput() - Method in interface org.intermine.webservice.server.lists.ListMaker
 
getInput() - Method in class org.intermine.webservice.server.lists.ListOperationService
 
getInput() - Method in class org.intermine.webservice.server.lists.ListsRequestParser
Returns parameters of web service as a parameter object.
getInput() - Method in class org.intermine.webservice.server.lists.ListSubtractionService
 
getInput() - Method in class org.intermine.webservice.server.lists.ListUploadService
Parse the parameters for this request.
getInput() - Method in class org.intermine.webservice.server.query.result.QueryResultRequestParser
Returns parsed parameters in parameter object - so this values can be easily get from this object.
getInput() - Method in class org.intermine.webservice.server.template.result.TemplateResultRequestParser
Returns parsed parameters in parameter object - so this values can be easily obtained from this object.
getInput(HttpServletRequest) - Method in class org.intermine.webservice.server.widget.WidgetsRequestParser
Returns parameters of web service as a parameter object.
getInputIdent() - Method in class org.intermine.api.bag.BagQueryResult.IssueResult
 
getInputIdentifiersForIssue(String) - Method in class org.intermine.api.bag.BagQueryResult
 
getInsertionLocationsResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Return a result set containing pairs of insertion feature_ids (eg. for "FBti0027974" => "FBti0023081") and the fmin and fmax of the first insertion in the pair (ie. the progenitor).
getInstance(ProfileManager) - Static method in class org.intermine.api.bag.SharedBagManager
Return the singleton SharedBagManager instance
getInstance() - Static method in class org.intermine.api.idresolution.IDResolver
 
getInstance(InterMineAPI, Properties) - Static method in class org.intermine.api.mines.FriendlyMineManager
Get an instance of FriendlyMineManager.
getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.KeySearchTracker
Return an instance of the KeySearchTracker
getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.ListTracker
Return an instance of the ListTracker
getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.LoginTracker
Return an instance of the LoginTracker
getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.QueryTracker
Return an instance of the QueryTracker
getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.TemplateTracker
Return an instance of the TemplateTracker
getInstance(String, Properties) - Static method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Creates a new instance of this class, given the properties defining it.
getInstance(String, Properties, Class<? extends IntegrationWriterDataTrackingImpl>, Class<? extends DataTracker>) - Static method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Creates a new IntegrationWriter instance of the specified class and with a specified DataTracker class plus properties.
getInstance(String, Properties) - Static method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Gets an ObjectStoreFastCollectionsForTranslatorImpl instance for the given properties
getInstance(String, Properties) - Static method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Gets an ObjectStoreFastCollectionsImpl instance for the given properties
getInstance(String, Properties) - Static method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets a ObjectStoreInterMineImpl instance for the given underlying properties
getInstance(String, Properties) - Static method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Gets an ObjectStore for the given underlying properties.
getInstance() - Static method in class org.intermine.pathquery.PathLengthComparator
 
getInstance(Database) - Static method in class org.intermine.sql.precompute.OptimiserCache
Returns an OptimiserCache object relevant to the database given.
getInstance(Connection) - Static method in class org.intermine.sql.precompute.PrecomputedTableManager
Gets a PrecomputedTableManager instance for the given underlying Connection.
getInstance(Database) - Static method in class org.intermine.sql.precompute.PrecomputedTableManager
Gets a PrecomputedTableManager instance for the given underlying database.
getInstance(String, Connection) - Static method in class org.intermine.sql.query.ExplainResult
Constructs an instance of ExplainResult for a given query String and database Connection.
getInstance(Query, Connection) - Static method in class org.intermine.sql.query.ExplainResult
Constructs an instance of ExplainResult for a given Query and database Connection.
getInstance(PreparedStatement) - Static method in class org.intermine.sql.query.ExplainResult
Constructs an instance of ExplainResult given a PreparedStatement object.
getInstance() - Static method in class org.intermine.util.AlwaysSet
Returns a new AlwaysSet with the correct type parameters.
getInstance() - Static method in class org.intermine.util.IdentityMap
Obtain an instance of this class
getInstance() - Static method in class org.intermine.util.ShutdownHook
Get the instance of this ShutdownHook.
getInstance(WebConfig, InterMineAPI) - Static method in class org.intermine.web.displayer.DisplayerManager
Fetch the DisplayerManager, a single instance is held.
getInstance(Properties) - Static method in class org.intermine.web.logic.help.HintManager
Return an instance of a HintManager.
getInstance() - Static method in class org.intermine.webservice.server.user.DeletionTokens
 
getInstanceByName(String) - Static method in class org.intermine.metadata.Model
Return a Model for specified model name (loading Model if necessary)
getInt(String) - Method in class org.intermine.webservice.client.results.Item
Get a property known to be an integer.
getIntegrationWriter() - Method in class org.intermine.dataloader.DataLoader
Return the IntegrationWriter that was passed to the constructor.
getIntegrationWriter(String) - Static method in class org.intermine.dataloader.IntegrationWriterFactory
Return an IntegrationWriter configured using properties file
getIntegrationWriter() - Method in class org.intermine.task.DirectDataLoaderTask
Return the IntegrationWriter for this task.
getInteractionResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Return a result set containing the interaction genes pairs, the title of the publication that reported the interaction and its pubmed id.
getInterMineAPI() - Static method in class org.intermine.web.context.InterMineContext
 
getInterMineAPI(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the InterMineAPI which provides access to core features of an InterMine application.
getInterMineAPI(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the InterMineAPI which provides the core features of an InterMine application.
getInterMineAPI(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the InterMineAPI which provides access to core features of an InterMine application.
getInterMineResults() - Method in class org.intermine.api.results.WebResults
Return the underlying results object.
getIntParameter(String) - Method in class org.intermine.webservice.server.WebService
Get the value of a parameter that should be interpreted as an integer.
getIntParameter(String, Integer) - Method in class org.intermine.webservice.server.WebService
Get the value of a parameter that should be interpreted as an integer.
getIntResponse(Request) - Method in class org.intermine.webservice.client.core.Service
Performs the request and returns the result as an integer.
getIntro(Command) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
getIntrons() - Method in class org.intermine.bio.web.model.GeneModel
Get the introns if present.
getIntroText() - Method in class org.intermine.web.logic.aspects.Aspect
Get the introduction text.
getIntSessionProperty(HttpSession, String, int) - Static method in class org.intermine.web.logic.WebUtil
Lookup an Integer property from the SessionContext and return it.
getInvalidBags() - Method in class org.intermine.api.profile.BagSet
 
getInvalidBags() - Method in class org.intermine.api.profile.Profile
 
getInvalidQuery() - Method in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
getInvalidQuery() - Method in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
getInvalidQuery() - Method in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
 
getInvalidSpans() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
 
getInvite() - Method in class org.intermine.web.struts.InvitationForm
 
getInviteData(ProfileManager, Profile) - Static method in class org.intermine.api.bag.SharingInvite
 
getInvitee() - Method in class org.intermine.api.bag.SharingInvite
 
getInvitee() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
getInviterId() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
getInvites(InterMineAPI, Profile) - Static method in class org.intermine.api.bag.SharingInvite
Get the invitations this profile has made.
getInvites(ProfileManager, BagManager, Profile) - Static method in class org.intermine.api.bag.SharingInvite
Get the invitations this profile has made.
getInwardIndirectionColumnName(CollectionDescriptor, int) - Static method in class org.intermine.sql.DatabaseUtil
Creates a column name for the "inward" key of a many-to-many collection descriptor.
getIqlQuery() - Method in class org.intermine.objectstore.query.Query
Returns an IqlQuery object representing this query, that may have been cached.
getIsApe() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionType
 
getIsDottedPath() - Method in class org.intermine.web.logic.config.FieldConfig
 
getIsKeyField() - Method in class org.intermine.web.logic.results.InlineTableResultElement
 
getIsNull() - Method in class org.intermine.web.logic.query.MetadataNode
 
getIsoforms() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getIsoformSynonyms() - Method in class org.intermine.bio.dataconversion.UniprotEntry
if an isoform has two ID tags, then the first one is used and the second one is added as a synonym
getIsRelative() - Method in class org.intermine.web.logic.WebUtil.HeadResource
 
getIssueIds() - Method in class org.intermine.api.bag.BagQueryResult
Get ids of all InterMineObjects returned that were issues for this bag query lookup.
getIssueIds(String) - Method in class org.intermine.api.bag.BagQueryResult
Get ids of all InterMineObjects returned that were registered as issues of this particular type for this bag query lookup.
getIssuer() - Method in class org.intermine.webservice.server.JWTVerifier.Verification
 
getIssueResults(String) - Method in class org.intermine.api.bag.BagQueryResult
 
getIssues() - Method in class org.intermine.api.bag.BagQueryResult
Get any results that require some user input before adding to the bag.
getItem() - Method in class org.intermine.api.search.SearchResult
Get the web searchable item that was found.
getItemElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
getItemElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
 
getItemRgb() - Method in class org.intermine.bio.io.bed.BEDRecord
 
getItemRgb() - Method in class org.intermine.bio.io.gaf.GAFRecord
 
getItems() - Method in class org.intermine.api.lucene.KeywordSearchFacet
list of all values and counts
getItems() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Return all items set and created in handler in this run - excludes sequence and ComputationalAnalysis items.
getItems() - Method in class org.intermine.dataconversion.MockItemWriter
Get the items that have been stored This method is not part of ItemWriter, and for testing convenience returns XML Items
getItems() - Method in class org.intermine.web.logic.results.InlineList
 
getItems() - Method in class org.intermine.web.logic.results.InlineResultsTableRow
 
getItems() - Method in class org.intermine.xml.full.FullHandler
Return the Items that have been read with this handler.
getItemWriter() - Method in class org.intermine.bio.dataconversion.ChadoProcessor
Return an ItemWriter used to handle the resultant Items
getItemWriter() - Method in class org.intermine.dataconversion.DataConverter
Return the ItemWriter that was passed to the constructor.
getIterator() - Method in class org.intermine.webservice.client.results.JSONResult
 
getIterator() - Method in class org.intermine.webservice.client.results.TabTableResult
Get a memory efficient iterator over the result rows as lists
getIterator() - Method in class org.intermine.webservice.client.results.XMLTableResult
getJavaClass() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the Java class name of the controller for this displayer.
getJBrowseTracks() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Get jbrowse track information from web.properties
getJobById(UUID) - Method in class org.intermine.api.idresolution.IDResolver
 
getJobById(String) - Method in class org.intermine.api.idresolution.IDResolver
 
getJobs() - Method in class org.intermine.api.idresolution.IDResolver
 
getJoinPath() - Method in class org.intermine.webservice.server.core.SubTable
 
getJoinType() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
getJson() - Method in class org.intermine.pathquery.PathQuery
toJson synonym for JSPs.
getJSONResponse(Request) - Method in class org.intermine.webservice.client.services.AbstractQueryService
Performs the request and returns a JSONResult containing the data.
getJSONResults(PathQuery, Page) - Method in class org.intermine.webservice.client.services.QueryService
 
getJSONResults(String, Page) - Method in class org.intermine.webservice.client.services.QueryService
Fetch some results as a list of JSON Objects.
getJSONResults(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService
Returns a subset of the results for the given template template with the given parameters, as JSON objects (see @link {http://www.intermine.org/wiki/JSONObjectFormat}).
getJSONResults(TemplateQuery, Page) - Method in class org.intermine.webservice.client.services.TemplateService
 
getJspName() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the name of the JSP associated with this displayer.
getJspPage() - Method in class org.intermine.web.displayer.ReportDisplayer
The JSP page that will be called with the request to render output.
getKey() - Method in interface org.intermine.util.ReferenceMap.ReferenceWithKey
Returns the key in the entry.
getKey() - Method in class org.intermine.web.logic.WebUtil.HeadResource
 
getKey() - Method in class org.intermine.webservice.server.core.Pair
 
getKeyFieldNames(Map<String, List<FieldDescriptor>>, String) - Static method in class org.intermine.api.config.ClassKeyHelper
Return names of the key fields for a given class.
getKeyFieldNames() - Method in class org.intermine.api.profile.InterMineBag
Return a list containing the keyFieldNames for the bag
getKeyFields(Map<String, List<FieldDescriptor>>, String) - Static method in class org.intermine.api.config.ClassKeyHelper
Return the key fields of a given class.
getKeyFields() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return the key fields for this path as a formatted string, for use in LOOKUP help message.
getKeyFields() - Method in class org.intermine.web.search.KeywordSearchResult
key field expressions
getKeyFieldValue(FastPathObject, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.config.ClassKeyHelper
Get a key field value for the given object.
getKeyFieldValues(FastPathObject, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.config.ClassKeyHelper
Get a list of key field values for the given object.
getKeyProperties(Source) - Static method in class org.intermine.dataloader.DataLoaderHelper
Return the Properties that enumerate the keys for this Source
getKeyProperties(String) - Static method in class org.intermine.metadata.PrimaryKeyUtil
Return the Properties that specify the key fields for the classes in this Model
getKeyStore() - Static method in class org.intermine.web.context.InterMineContext
 
getKeywords() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getKeywordSearches(Connection) - Method in class org.intermine.api.tracker.KeySearchTracker
Return the number of search for each keyword
getKeywordSearches() - Method in class org.intermine.api.tracker.TrackerDelegate
Return the number of search for each keyword
getLabel() - Method in class org.intermine.web.logic.config.FieldConfig
The human readable label for this field.
getLabel() - Method in class org.intermine.web.logic.config.Type
Get the label property's value.
getLabel() - Method in class org.intermine.web.logic.query.DisplayConstraint.DisplayConstraintOption
Get the value to be displayed in the dropdown for this operation.
getLabel() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getLabel() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
label for the results table.
getLabel() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
Get the label for this trail element.
getLabels() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
Get additional display labels for attribute values in the enrichment analysis, these may be names where the values analysed were identifiers.
getLabels() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
 
getLabels() - Method in class org.intermine.web.logic.widget.EnrichmentResults
Get additional display labels for attribute values in the enrichment analysis, these may be names where the values analysed were identifiers.
getLabels(GraphWidgetConfig) - Method in class org.intermine.webservice.server.widget.WidgetProcessorImpl
Get the labels for Graph widgets.
getLabs(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return the lab name.
getLargeImage() - Method in class org.intermine.web.logic.aspects.Aspect
Webapp relative path to large image.
getLastClassDescriptor() - Method in class org.intermine.pathquery.Path
Returns the last ClassDescriptor in the path.
getLastClassName() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Fetch the unqualified class name of the final class on this path, if the path represents an attribute this will be the parent class of that attribute.
getLastElement() - Method in class org.intermine.pathquery.Path
Return the last string element of this path, throw an exception of there is only one element, i.e. for 'Company.departments.manager' return 'manager'.
getLayout() - Method in class org.intermine.web.logic.template.TemplateResultInput
 
getLayout() - Method in class org.intermine.webservice.server.query.result.QueryResultInput
 
getLdr() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
getLeft() - Method in class org.intermine.objectstore.query.OverlapConstraint
Returns the left OverlapRange.
getLeft() - Method in class org.intermine.sql.query.Constraint
Returns the left argument of the constraint.
getLeft() - Method in class org.intermine.sql.query.InListConstraint
Returns the left AbstractValue.
getLeft() - Method in class org.intermine.sql.writebatch.Row
Returns left.
getLeftArgument(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Get the left argument of the given constraint, will return null if passed a ConstraintSet or a MultipleInBagConstraint.
getLeftColName() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Returns the left column name.
getLeftField() - Method in class org.intermine.api.query.range.ConstraintOptions
Defaults to "start".
getLeftOp() - Method in class org.intermine.api.query.range.ConstraintOptions
 
getLength() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getLength() - Method in class org.intermine.web.logic.results.InlineList
 
getLengthWithoutInit() - Method in class org.intermine.objectstore.query.ClobAccess
Returns the (possibly uninitialised) length internal parameter in this object, for use by subclass constructors.
getLevel() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
 
getLevelClass() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList.StainingLevel
Convert the overall staining level of all Expressions into an average (ceiled/floored) value
getLevelValue() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList.StainingLevel
Get the float value representing the average Expression level
getLibraryCVTermResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return the interesting rows from the librarycvterm table.
getLibraryFeatureResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return the interesting rows from the libraryprop table.
getLimit() - Method in class org.intermine.objectstore.query.Query
Returns the LIMIT parameter for this query.
getLimit() - Method in class org.intermine.sql.precompute.LimitOffsetQuery
Getter for limit.
getLimit() - Method in class org.intermine.sql.query.Query
Gets the LIMIT number for this query.
getLimit() - Method in class org.intermine.webservice.server.WebServiceInput
Returns maximum number of results the user will accept.
getLineBreak() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
getLineBreak() - Method in class org.intermine.webservice.server.WebService
 
getLineLength() - Method in class org.intermine.web.logic.config.InlineListConfig
 
getLineLength() - Method in class org.intermine.web.logic.results.InlineList
 
getLink() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
the link is the class that generates the url for each result.
getLink() - Method in class org.intermine.web.struts.WidgetForm
 
getLink() - Method in class org.intermine.web.tags.disclosure.DisclosureHeadTag
 
getLink() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Returns link switching between displayed and hidden state.
getLink(String, String, String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator
Generates QueryResultService web service link.
getLinkedFeature(String) - Method in class org.intermine.webservice.server.complexes.ExportService.FeatureHolder
 
getLinkPath(String, String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator
Get the link path for a query.
getLinkPath(TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Returns the path section of the link for this template.
getLinkPath(TemplateQuery, String) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Returns the path section of the link for this template.
getLinkPath(TemplateQuery, String, boolean) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Returns the path section of the link for this template.
getLinkRedirect() - Method in class org.intermine.api.results.ResultElement
 
getLinkRedirect() - Method in class org.intermine.web.search.KeywordSearchResult
URL set in web.properties.
getLinkRedirector() - Method in interface org.intermine.api.API
 
getLinkRedirector() - Method in class org.intermine.api.InterMineAPI
 
getLinks(MultiKey) - Method in class org.intermine.api.mines.FriendlyMineManager
 
getLinks(Mine, Mine, ObjectRequest) - Method in class org.intermine.bio.web.displayer.FriendlyMineLinkGenerator
 
getLinks(Mine, Mine, ObjectRequest) - Method in interface org.intermine.web.displayer.InterMineLinkGenerator
Query other intermines for this object
getLinks(FriendlyMineManager, String, String, String) - Method in class org.intermine.web.util.InterMineLinkGenerator
Query other intermines for this object
getList(String, String) - Method in class org.intermine.web.autocompletion.AutoCompleter
returns a string array with the search results of the query in the field
getList(String) - Method in class org.intermine.webservice.client.services.ListService
Returns an object representing a list on the server.
getList(Profile, String) - Method in class org.intermine.webservice.server.query.QueryListAppendService
Get a list from a profile, throwing a service forbidden exception if the list is not accessible.
getListCreationTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices
 
getListCreationTrend() - Method in class org.intermine.dwr.TrackAjaxServices
 
getListExecutionTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices
 
getListExecutionTrend() - Method in class org.intermine.dwr.TrackAjaxServices
 
getListIterator() - Method in class org.intermine.webservice.client.results.RowResultSet
Get a memory efficient iterator over the result rows as lists
getListLeft() - Method in class org.intermine.web.struts.ModifyBagForm
 
getListManager() - Method in class org.intermine.webservice.server.WebService
 
getListMap() - Method in class org.intermine.webservice.client.services.ListService
Returns a map from list-name to list.
getListMap() - Method in class org.intermine.webservice.server.core.ListManager
Returns the lists available to the current user in a Map.
getListName() - Method in class org.intermine.webservice.server.lists.ListInput
 
getListOfTypes() - Method in class org.intermine.web.logic.results.InlineResultsTable
 
getListOperations(Connection) - Method in class org.intermine.api.tracker.ListTracker
Return the operations done for each list (execution or creation)
getListOperations() - Method in class org.intermine.api.tracker.TrackerDelegate
Return the operations done for each list (execution or creation)
getListPath() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
getListRight() - Method in class org.intermine.web.struts.ModifyBagForm
 
getLists() - Method in class org.intermine.webservice.server.core.ListManager
Returns the lists available to the current user.
getLists() - Method in class org.intermine.webservice.server.lists.AsymmetricOperationInput
 
getLists() - Method in class org.intermine.webservice.server.lists.AvailableListsService
Get the lists for this request.
getLists() - Method in class org.intermine.webservice.server.lists.ListInput
 
getLists() - Method in class org.intermine.webservice.server.lists.ListsService
Executes service specific logic.
getListsButton() - Method in class org.intermine.web.struts.ModifyBagForm
 
getListsContaining(Integer) - Method in class org.intermine.webservice.server.core.ListManager
Returns the current lists available to the current user which contain the specified object.
getListService() - Method in class org.intermine.webservice.client.core.ServiceFactory
Return a new ListService for getting getting list information from.
getListsMatching(ListManager, String) - Method in class org.intermine.webservice.server.lists.AvailableListsService
Get the lists that match the current filter.
getListsNames(Integer) - Method in class org.intermine.webservice.server.core.ListManager
Returns public current lists that contain object with specified id.
getListsWithObject(String, String) - Method in class org.intermine.webservice.client.services.ListService
Returns all accessible InterMine lists containing the object corresponding to the specified publicId.
getListsWithObject(int) - Method in class org.intermine.webservice.client.services.ListService
Returns all accessible InterMine public lists containing the object with the specified DB identifier.
getListUploadTokeniser() - Static method in class org.intermine.api.query.LookupTokeniser
Return a tokeniser suitable for parsing tokens received from a list upload context.
getLocalMine() - Method in class org.intermine.api.mines.FriendlyMineManager
 
getLocatedGenesResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Return from chado the feature_ids of the genes with entries in the featureloc table.
getLocation() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Return the location Item set by setLocation()
getLocation() - Method in class org.intermine.task.project.Source
Get the directory that contains this Source.
getLocation() - Method in class org.intermine.task.project.UserProperty
Get the location
getLocationFromHeader(String, SequenceFeature, Organism) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask
Return a Location object create by parsing the useful information from a FlyBase fasta header line.
getLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Returns the log used by this objectstore.
getLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Returns the log used by this objectstore.
getLogarithmMap(String, TemplateManager) - Method in class org.intermine.api.tracker.TemplatesExecutionMap
Return a map containing the logarithm's sum of the templates executions launched by the same users or during the same sessions.
getLogarithmMap(String, String, TemplateManager) - Method in class org.intermine.api.tracker.TemplateTracker
Return a map containing the logarithm of accesses for each template.
getLogBeforeExecute() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets the logBeforeExecute configuration option.
getLogBeforeExecute() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Gets the logBeforeExecute configuration option.
getLogEverything() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets the logEverything configuration option.
getLogEverything() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Gets the logEverything configuration option.
getLogExplains() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets the logExplains configuration option.
getLogExplains() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Gets the logExplains configuration option.
getLogicExpression() - Method in class org.intermine.pathquery.PathQuery
 
getLoginTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices
 
getLogo() - Method in class org.intermine.api.mines.LocalMine
 
getLogo() - Method in interface org.intermine.api.mines.Mine
 
getLogo() - Method in class org.intermine.api.mines.RemoteMine
 
getLongDisplayers() - Method in class org.intermine.web.logic.config.Type
Get the List of long Displayers
getLookupOp() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return the LOOKUP constraint op.
getLookupOs() - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Returns the objectstore that contains the equivalent objects.
getLookupTokeniser() - Static method in class org.intermine.api.query.LookupTokeniser
Return a tokeniser suitable for parsing tokens received from a lookup constraint context.
getLoopPath() - Method in class org.intermine.pathquery.PathConstraintLoop
Returns the path that the constraint is constraining to.
getLoopQueryOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of loopQueryOp
getLoopQueryOps() - Method in class org.intermine.web.logic.query.DisplayConstraint
Returns the set of operators valid for loop constraints.
getLoopQueryValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of loopQueryValue
getMailinglist() - Method in class org.intermine.web.struts.CreateAccountForm
 
getMainIds() - Method in class org.intermine.bio.dataconversion.GeneInfoRecord
Return the entrez gene id, official symbol and default symbol (if different).
getMainSetOp() - Method in class org.intermine.api.query.range.ConstraintOptions
 
getMainSource(String, String) - Method in interface org.intermine.dataloader.IntegrationWriter
Converts a string describing the data source into a Source object suitable for passing to the store method as the main source.
getMainSource(String, String) - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Converts a string describing the data source into a Source object suitable for passing to the store method as the main source.
getMainTitles() - Method in class org.intermine.web.logic.config.Type
 
getMakeUcscCompatible() - Method in class org.intermine.bio.web.struts.BEDExportForm
Return whether to make exported BED compatible with UCSC genome browser.
getMap() - Method in class org.intermine.util.DynamicBean
Getter for the map, for testing purposes
getMapIterator() - Method in class org.intermine.webservice.client.results.RowResultSet
Get a memory efficient iterator over the result rows as lists
getMapper(TagMapper.Field) - Static method in class org.intermine.api.profile.TagMapper
Get a tag mapper.
getMatchAndIssueIds() - Method in class org.intermine.api.bag.BagQueryResult
Get ids of all InterMineObjects returned that were matches or issues for this bag query lookup.
getMatchedBaseCount(GenomicRegion, List<String>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Calculate the number of matched bases.
getMatcher() - Method in class org.intermine.webservice.server.lists.ListUploadService
Get the String Matcher for parsing the list of identifiers.
getMatches() - Method in class org.intermine.api.bag.BagQueryResult
Get any exact matches found by the queries [id -> [input strings].
getMatchIDs() - Method in class org.intermine.web.struts.BagUploadConfirmForm
Get the encoded match ids (hidden form field).
getMatchLocResultSet(Connection, String) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Return the interesting feature (EST, UST, RST, other?)
getMatchLocResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return the interesting matches from the featureloc and feature tables.
getMatchOnFirst() - Method in class org.intermine.api.bag.BagQueryConfig
If flag is true, bagqueryrunner queries for identifier until match is found, returning only that first matching record.
getMatchTypesResultSet(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Return the match types, used to determine which additional query to run This is a protected method so that it can be overridden for testing
getMaterialisedCollection() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Gets the collection if it is a real materialised collection.
getMax(String) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask
Return the maximum coordinate of the given location
getMax() - Method in class org.intermine.objectstore.query.ResultsInfo
Returns the maximum possible number of rows in the results.
getMax() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
maximum value to display.
getMax() - Method in class org.intermine.web.struts.WidgetForm
 
getMax() - Method in class org.intermine.webservice.client.services.QueryService.NumericSummary
 
getMaxLimit() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Get the maximum LIMIT that can be used in an SQL query without throwing an ObjectStoreLimitReachedException
getMaxLimit() - Method in interface org.intermine.objectstore.ObjectStore
Get the maximum LIMIT that can be used in an SQL query without throwing an ObjectStoreLimitReachedException
getMaxLimit() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Get the maximum LIMIT that can be used in an SQL query without throwing an ObjectStoreLimitReachedException
getMaxLimit() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Get the maximum LIMIT that can be used in an SQL query without throwing an ObjectStoreLimitReachedException
getMaxOffset() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Get the maximum range start index a that can be accessed in a Results object without throwing an ObjectStoreLimitReachedException
getMaxOffset() - Method in interface org.intermine.objectstore.ObjectStore
Get the maximum range start index a that can be accessed in a Results object without throwing an ObjectStoreLimitReachedException
getMaxOffset() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Get the maximum range start index a that can be accessed in a Results object without throwing an ObjectStoreLimitReachedException
getMaxOffset() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Get the maximum range start index a that can be accessed in a Results object without throwing an ObjectStoreLimitReachedException
getMaxParam() - Method in class org.intermine.objectstore.query.WidthBucketFunction
 
getMaxPValue() - Method in interface org.intermine.web.logic.widget.EnrichmentOptions
 
getMaxPValue() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
getMaxQueryParseTime() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
getMaxQueryParseTime() - Method in class org.intermine.sql.precompute.QueryOptimiserContext
Get the maximum time in milliseconds that the optimiser should spend parsing a query from SQL string to an org.intermine.sql.Query object.
getMaxRetrievableIndex() - Method in class org.intermine.api.results.WebResults
Returns the ObjectStore's maximum allowable offset.
getMaxRetrievableIndex() - Method in interface org.intermine.api.results.WebTable
Return the maximum retrievable index for this PagedTable.
getMaxRetrievableIndex() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return the maximum retrievable index for this PagedTable.
getMaxSize() - Method in class org.intermine.objectstore.query.ResultsBatches
Returns the current maximum number of rows in the results
getMaxTime() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException
getMaxTime() - Method in interface org.intermine.objectstore.ObjectStore
Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException
getMaxTime() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException
getMaxTime() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException
getMaxValues() - Method in class org.intermine.objectstore.ObjectStoreSummary
Return the configured maximum number of values to show in a dropdown.
getMd5checksum() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getMd5checksum(String) - Static method in class org.intermine.metadata.Util
 
getMessage() - Method in class org.intermine.api.bag.BagQuery
Return the message that was passed to the constructor.
getMessage() - Method in class org.intermine.web.struts.ContactForm
 
getMessage() - Method in exception org.intermine.webservice.client.exceptions.ResultException
getMessage() - Method in exception org.intermine.webservice.client.exceptions.ServiceException
getMessage() - Method in exception org.intermine.webservice.server.exceptions.ServiceException
getMessageElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
getMessageElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
 
getMessageFormat() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
 
getMessageFormat() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
 
getMessageFormat() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
 
getMethod() - Method in class org.intermine.bio.dataconversion.UniprotConfig.IdentifierConfig
 
getMethodDescriptors() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getMethodDescriptors() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getMimeType() - Method in enum org.intermine.api.mines.ContentType
 
getMin(String) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask
Return the minimum coordinate of the given location
getMin() - Method in class org.intermine.objectstore.query.ResultsInfo
Returns the minimum possible number of rows in the results.
getMin() - Method in class org.intermine.webservice.client.services.QueryService.NumericSummary
 
getMinBagTableSize() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Returns the cutoff value used to decide if a bag should be put in a table.
getMinBagTableSize() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Returns the cutoff value used to decide if a bag should be put in a table.
getMine(String) - Method in class org.intermine.api.mines.FriendlyMineManager
 
getMineId() - Method in class org.intermine.webservice.server.lists.ListsServiceInput
 
getMineResultsLink(String, String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator
Get the link for a query that shows the results in a mine.
getMineResultsLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Get a link that takes the user to a results page in the originating mine.
getMineResultsPath(String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator
Get the link path for a query that shows the results in a mine.
getMineResultsPath(TemplateQuery, boolean) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Get a link that takes the user to a results page in the originating mine.
getMinimalPath() - Method in class org.intermine.pathquery.Node
 
getMinParam() - Method in class org.intermine.objectstore.query.WidthBucketFunction
 
getMinSize() - Method in class org.intermine.objectstore.query.ResultsBatches
Returns the current minimum number of rows in the results
getMissingTables() - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns the Set of table names which are tables missing from the database.
getMockIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a mock id resolver for unit test
getMode() - Method in class org.intermine.sql.precompute.QueryOptimiserContext
Returns the optimiser mode of operation.
getModel() - Method in interface org.intermine.api.API
 
getModel() - Method in class org.intermine.api.InterMineAPI
 
getModel() - Method in class org.intermine.api.mines.LocalMine
 
getModel() - Method in interface org.intermine.api.mines.Mine
Get the main model associated with this application.
getModel() - Method in class org.intermine.api.mines.RemoteMine
 
getModel() - Method in class org.intermine.bio.dataconversion.ChadoProcessor
Return the Model of the target database.
getModel() - Method in class org.intermine.bio.ontology.SequenceOntology
 
getModel() - Method in class org.intermine.dataconversion.DataConverter
Return the data Model that was passed to the constructor.
getModel() - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Returns the Model used.
getModel() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Return the metadata associated with this ObjectStore
getModel() - Method in class org.intermine.metadata.ClassDescriptor
Return the model this class is a part of.
getModel() - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns the model.
getModel() - Method in interface org.intermine.objectstore.ObjectStore
Return the metadata associated with this ObjectStore
getModel() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Return the metadata associated with this ObjectStore
getModel() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Return the metadata associated with this ObjectStore
getModel() - Method in class org.intermine.pathquery.Path
Return the model that this path is created for.
getModel() - Method in class org.intermine.pathquery.PathQuery
Returns the Model object stored in this object.
getModel() - Method in class org.intermine.webservice.client.core.ServiceFactory
A convenience method to getting a model (used widely throughout the API).
getModel() - Method in class org.intermine.webservice.client.services.ModelService
Returns the model used by the InterMine instance which the service is connected to.
getModel() - Method in class org.intermine.xml.full.Item
Return the model that was passed to the constructor or set with setModel().
getModelFromClasspath(String, Properties) - Static method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Read the Model from the classpath.
getModelName() - Method in class org.intermine.task.ConverterTask
Return the model name
getModelService() - Method in class org.intermine.webservice.client.core.ServiceFactory
Return a new ModelService for retrieving the data model.
getModelXml() - Method in class org.intermine.webservice.client.services.ModelService
An method used internally to fetch the XML for the model from the server.
getModifiableEditableConstraints() - Method in class org.intermine.template.TemplateQuery
Returns the list of all editable constraints.
getMolecularWeight() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getMonkey() - Method in class org.intermine.web.struts.ContactForm
 
getMostPopularTemplateOrder(Integer) - Method in class org.intermine.api.template.TemplateManager
Return the list of public templates ordered by rank descendant.
getMostPopularTemplateOrder(String, String, Integer) - Method in class org.intermine.api.template.TemplateManager
Return the template list ordered by rank descendant for the user/sessionid specified in the input
getMouseIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a mouse id resolver
getMouseIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a mouse id resolver
getMouseIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a mouse id resolver
getMrlv() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
Returns the MultiRowLaterValue corresponding to this object.
getMRNA(String, Organism, Model) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask
Create an MRNA with the given primaryIdentifier and organism or return null of MRNA is not in the data model.
getMultiValueAttribute() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Returs the value of multiValueAttribute
getMultiValueAttribute() - Method in class org.intermine.web.struts.TemplateForm
Returns the multivalueattribute
getMultiValueAttribute(String) - Method in class org.intermine.web.struts.TemplateForm
Returns the multivalueattribute given a key
getMultiValues() - Method in class org.intermine.web.logic.query.DisplayConstraint
Returns the value collection if the constraint is a multivalue, otherwise return null.
getMultivalues() - Method in class org.intermine.web.logic.template.ConstraintInput
Return multivalues
getMultiValues() - Method in class org.intermine.web.struts.TemplateForm
Returns the multiValues
getMultiValues(String) - Method in class org.intermine.web.struts.TemplateForm
Get a multi value
getMultiValuesAsString() - Method in class org.intermine.web.logic.query.DisplayConstraint
If the constraint is a multivalue, returns the value collection represented as string separated by ', ', otherwise return an empty String.
getName() - Method in class org.intermine.api.beans.ObjectDetails
 
getName() - Method in class org.intermine.api.lucene.KeywordSearchFacet
user-friendly name
getName() - Method in class org.intermine.api.lucene.KeywordSearchFacetData
name of the facet (displayed on page)
getName() - Method in class org.intermine.api.mines.LocalMine
 
getName() - Method in interface org.intermine.api.mines.Mine
 
getName() - Method in class org.intermine.api.mines.RemoteMine
 
getName() - Method in class org.intermine.api.profile.InterMineBag
Returns the value of name
getName() - Method in class org.intermine.api.profile.InvalidBag
 
getName() - Method in class org.intermine.api.profile.Profile
Return a first part of the username before the "@" sign (used in metabolicMine)
getName() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
 
getName() - Method in class org.intermine.api.profile.SavedQuery
Get the name of the saved query.
getName() - Method in class org.intermine.api.profile.StorableBag
 
getName() - Method in interface org.intermine.api.profile.Taggable
The name (or identifier) used as the primary key for storing this object.
getName() - Method in exception org.intermine.api.query.BagNotFound
 
getName() - Method in class org.intermine.api.results.Column
Get the name (title) of the column.
getName() - Method in class org.intermine.api.tracker.AbstractTracker
Return the tracker's name
getName() - Method in class org.intermine.api.tracker.KeySearchTracker
 
getName() - Method in class org.intermine.api.tracker.ListTracker
Return the tracker's name
getName() - Method in class org.intermine.api.tracker.LoginTracker
Return the tracker's name
getName() - Method in class org.intermine.api.tracker.QueryTracker
Return the tracker's name
getName() - Method in class org.intermine.api.tracker.TemplateTracker
Return the tracker's name
getName() - Method in interface org.intermine.api.tracker.Tracker
Return the tracker's name
getName() - Method in class org.intermine.bio.chado.ChadoCVTerm
Return the name of this term.
getName() - Method in class org.intermine.bio.dataconversion.UniprotConverter.DiseaseHolder
 
getName() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getName() - Method in class org.intermine.bio.io.bed.BEDRecord
 
getName() - Method in class org.intermine.bio.io.gaf.GAFRecord
 
getName() - Method in class org.intermine.bio.ontology.OboTerm
Get the name of this term.
getName() - Method in class org.intermine.bio.ontology.OboTermSynonym
Get the synonym name.
getName() - Method in class org.intermine.bio.ontology.OboTypeDefinition
 
getName() - Method in class org.intermine.dataloader.Source
Getter for name.
getName() - Method in class org.intermine.metadata.ClassDescriptor
Returns the fully qualified class name described by this ClassDescriptor.
getName() - Method in class org.intermine.metadata.FieldDescriptor
Get the name of the described field.
getName() - Method in class org.intermine.metadata.Model
Get the name of this model - i.e. package name.
getName() - Method in class org.intermine.metadata.PrimaryKey
Return the name
getName() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the field name
getName() - Method in class org.intermine.pathquery.LogicExpression.Variable
Get variable name.
getName() - Method in class org.intermine.sql.Database
Gets the database name only, not the full URL.
getName() - Method in class org.intermine.sql.precompute.PrecomputedTable
Gets the name of this PrecomputedTable
getName() - Method in class org.intermine.sql.query.Field
Returns the name of the field.
getName() - Method in class org.intermine.sql.query.Table
Returns the name of the table
getName() - Method in class org.intermine.task.project.Source
Get the name of this object.
getName() - Method in class org.intermine.task.project.UserProperty
Return the name
getName() - Method in class org.intermine.template.TemplateQuery
Get the query short name.
getName() - Method in class org.intermine.web.logic.aspects.Aspect
Get the name of the data set.
getName() - Method in class org.intermine.web.logic.aspects.AspectSource
Get the source name.
getName() - Method in class org.intermine.web.logic.results.ReportObjectField
Get field name
getName() - Method in class org.intermine.web.logic.template.TemplateResultInput
Returns template name.
getName() - Method in class org.intermine.web.struts.ContactForm
 
getName() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
 
getName() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
 
getName() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
 
getName() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
 
getName() - Method in class org.intermine.web.struts.TemplateForm
Get the template name.
getName() - Method in class org.intermine.web.struts.TemplateSettingsForm
 
getName() - Method in class org.intermine.webservice.client.lists.ItemList
Get the name of this list.
getName() - Method in class org.intermine.webservice.client.widget.Widget
 
getName() - Method in class org.intermine.xml.full.Attribute
Get the name of this field
getName() - Method in class org.intermine.xml.full.Reference
Get the name of this field
getName() - Method in class org.intermine.xml.full.ReferenceList
Get the name of this field.
getNames() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the list of the Name field from the attributes of this record.
getNameSource() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
 
getNamespace() - Method in class org.intermine.bio.ontology.OboTerm
Get the namespace attribute.
getNewBagName() - Method in class org.intermine.api.bag.operations.BagOperation
 
getNewBagName() - Method in class org.intermine.web.struts.BagUploadConfirmForm
Get the bag name.
getNewBagName() - Method in class org.intermine.web.struts.ModifyBagForm
Get the new bag name.
getNewBagName() - Method in class org.intermine.web.struts.SaveBagForm
Gets the value of newBagName
getNewBagType() - Method in class org.intermine.api.bag.operations.BagOperation
 
getNewBagType() - Method in class org.intermine.api.bag.operations.Intersection
 
getNewBagType() - Method in class org.intermine.api.bag.operations.RelativeComplement
 
getNewBagType() - Method in class org.intermine.api.bag.operations.SymmetricDifference
 
getNewBagType() - Method in class org.intermine.api.bag.operations.Union
 
getNewBagType() - Method in class org.intermine.web.struts.TriageBagForm
Get the new bag name.
getNewData() - Method in class org.intermine.dataloader.ObjectDescription
Returns the new data, which needs to be written back into the backing database.
getNewId() - Method in class org.intermine.web.struts.oauth2.MigrationMapping
 
getNewIds(InterMineObject, ObjectStore) - Method in interface org.intermine.api.bag.IdUpgrader
For the given object from an old ObjectStore, find the corresponding InterMineObjects in a new ObjectStore.
getNewIds(InterMineObject, ObjectStore) - Method in class org.intermine.web.bag.PkQueryIdUpgrader
For the given object from an old ObjectStore, find the corresponding InterMineObjects in a new ObjectStore.
getNewListType(ListInput) - Method in class org.intermine.bio.webservice.GenomicRegionSearchService
 
getNewListType(ListInput) - Method in class org.intermine.webservice.server.lists.ListMakerService
Calculate the type of the new list.
getNewListType(ListInput) - Method in class org.intermine.webservice.server.lists.ListOperationService
 
getNewListType(ListInput) - Method in class org.intermine.webservice.server.lists.ListUploadService
 
getNewObject() - Method in class org.intermine.api.bag.ConvertedObjectPair
Get the newObject that was passed to the constructor.
getNewpassword() - Method in class org.intermine.web.struts.ChangePasswordForm
The new password
getNewpassword() - Method in class org.intermine.web.struts.PasswordResetForm
Gets the value of newpassword.
getNewpassword2() - Method in class org.intermine.web.struts.ChangePasswordForm
New password verification
getNewpassword2() - Method in class org.intermine.web.struts.PasswordResetForm
Gets the value of newpassword2.
getNewsPreview(String) - Static method in class org.intermine.dwr.AjaxServices
Work as a proxy for fetching remote file (RSS)
getNewTemplateQuery() - Method in class org.intermine.api.profile.TemplateQueryUpdate
 
getNewWriter() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Create an ObjectStoreWriter that writes into this ObjectStore.
getNewWriter() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Create an ObjectStoreWriter that writes into this ObjectStore.
getNewWriter() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Create an ObjectStoreWriter that writes into this ObjectStore.
getNewWriter() - Method in interface org.intermine.objectstore.ObjectStore
Create an ObjectStoreWriter that writes into this ObjectStore.
getNewWriter() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Create an ObjectStoreWriter that writes into this ObjectStore.
getNewWriter() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Create an ObjectStoreWriter that writes into this ObjectStore.
getNextLine() - Method in class org.intermine.webservice.client.results.ResultSet
Get the next line of results.
getNextLink(int) - Method in class org.intermine.web.tags.table.NavigationBarTag
 
getNicerDisplayerName() - Method in class org.intermine.web.displayer.ReportDisplayer
A JSP wants a nice name to display while the Displayer is loading
getNoConstraintsString() - Method in class org.intermine.pathquery.Path
Required for jsp
getNonXrefs() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
used for testing
getNoResultsMessage() - Method in class org.intermine.web.tags.table.TableTag
 
getNormalInlineLists() - Method in class org.intermine.web.logic.results.ReportObject
 
getNoseyObjectStore(ObjectStore) - Method in class org.intermine.dataloader.BatchingFetcher
Returns an ObjectStore layered on top of the given ObjectStore, which reports to this fetcher which objects are being loaded.
getNotAnalysed() - Method in class org.intermine.web.logic.widget.HTMLWidget
 
getNotAnalysed() - Method in class org.intermine.web.logic.widget.Widget
 
getNote() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the first value of the Note field from the attributes of this record.
getNullAttributes(String) - Method in class org.intermine.objectstore.ObjectStoreSummary
Get a list of the attributes that, for a given class, are always null or empty.
getNullConstraint() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Get the null/not null constraint value.
getNullConstraint() - Method in class org.intermine.web.struts.TemplateForm
Get the nullConstraint
getNullConstraint(String) - Method in class org.intermine.web.struts.TemplateForm
Get a nullConstraint
getNullReferencesAndCollections(String) - Method in class org.intermine.objectstore.ObjectStoreSummary
Get a list of the reference and collection names that, for a given class, are always null or empty.
getNumberOfBins() - Static method in class org.intermine.api.query.MainHelper.SummaryConfig
Returns the number of bins to split a histogram into.
getNumberOfMainTitlesToShow() - Method in class org.intermine.web.logic.config.HeaderConfigTitle
 
getNumberOfTableRowsToShow() - Method in class org.intermine.web.logic.results.ReportObject
The said function will resolve the maximum number of rows to show (in Collections) from webProperties.
getNumberOpt() - Method in class org.intermine.web.struts.WidgetForm
 
getNumericSummary(PathQuery, String) - Method in class org.intermine.webservice.client.services.QueryService
Get a summary for the values in column of a query.
getOAuth2Providers(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the set of accepted Open-ID providers.
getObject() - Method in class org.intermine.api.lucene.KeywordSearchHit
object
getObject() - Method in interface org.intermine.api.results.ResultCell
 
getObject() - Method in class org.intermine.api.results.ResultElement
Return the Object contained in this result element.
getoBJECT() - Method in interface org.intermine.model.InterMineFastPathObject
Returns the NotXml serialised version of this object.
getoBJECT() - Method in interface org.intermine.model.InterMineObject
Returns the NotXml serialised version of this object.
getObject() - Method in class org.intermine.objectstore.proxy.ProxyReference
Gets the real object from the database.
getoBJECT() - Method in class org.intermine.objectstore.proxy.ProxyReference
Returns the NotXml serialised version of this object.
getObject() - Method in class org.intermine.objectstore.query.ContainsConstraint
Returns the InterMineObject of the constraint.
getObject() - Method in class org.intermine.web.logic.config.InlineListObject
Fetch the InterMine object (if needed)
getObject() - Method in class org.intermine.web.logic.results.DisplayReference
Get the referenced object
getObject() - Method in class org.intermine.web.logic.results.ReportObject
Get InterMine object
getObject() - Method in class org.intermine.web.logic.TreeNode
Get the Object
getObject() - Method in class org.intermine.web.search.KeywordSearchResult
returns original intermine object
getObject() - Method in class org.intermine.webservice.server.core.TableCell
 
getObjectByExample(T, Set<String>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
getObjectByExample(T, Set<String>) - Method in interface org.intermine.objectstore.ObjectStore
Return an object from the objectstore that has the fields mentioned in the list set to the same values as the fields in the provided example object.
getObjectByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
getObjectByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Return an object from the objectstore that has the fields mentioned in the list set to the same values as the fields in the provided example object.
getObjectByExample(T, Set<String>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
 
getObjectById(Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Search database for object matching the given object id
getObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Search database for object matching the given object id and class
getObjectById(Integer) - Method in interface org.intermine.objectstore.ObjectStore
Get an object from the ObjectStore by giving an ID.
getObjectById(Integer, Class<? extends InterMineObject>) - Method in interface org.intermine.objectstore.ObjectStore
Get an object from the ObjectStore by giving an ID and a hint of the Class of the object.
getObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Get an object from the ObjectStore by giving an ID.
getObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Get an object from the ObjectStore by giving an ID and a hint of the Class of the object.
getObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Get an object from the ObjectStore by giving an ID.
getObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Get an object from the ObjectStore by giving an ID and a hint of the Class of the object.
getObjectHits - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
getObjectId() - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary
 
getObjectId() - Method in class org.intermine.web.logic.results.InlineResultsTableRow
Used from JSP
getObjectId() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
Get the object id for this trail element.
getObjectIds(BrowseHit[]) - Static method in class org.intermine.api.lucene.KeywordSearch
 
getObjectOps - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
getObjectPrefetches - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
getObjects() - Method in class org.intermine.api.beans.PartnerLink
 
getObjects(InterMineAPI, Set<Integer>) - Static method in class org.intermine.api.data.Objects
Resolve a set of ids to mapping from ID to object.
getObjects() - Method in class org.intermine.webservice.client.results.JSONResult
 
getObjectsByExample(T, Set<String>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
getObjectsByExample(T, Set<String>) - Method in interface org.intermine.objectstore.ObjectStore
Return an object from the objectstore that has the fields mentioned in the list set to the same values as the fields in the provided example object.
getObjectsByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
getObjectsByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
 
getObjectsByExample(T, Set<String>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
 
getObjectsByIds(Collection<Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Get an objects from the ObjectStore that have the IDs in the ids colection
getObjectsByIds(Collection<Integer>) - Method in interface org.intermine.objectstore.ObjectStore
Get an objects from the ObjectStore that have the IDs in the ids colection
getObjectsByIds(Collection<Integer>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Get an objects from the ObjectStore that have the IDs in the ids colection
getObjectsByIds(Collection<Integer>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Get an objects from the ObjectStore that have the IDs in the ids colection
getObjectStore() - Method in interface org.intermine.api.API
 
getObjectStore() - Method in class org.intermine.api.InterMineAPI
 
getObjectStore() - Static method in class org.intermine.api.query.PathQueryAPI
Returns the production ObjectStore configured in webapp.os.alias.
getObjectStore() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Retrieve this Writer's ObjectStore.
getObjectStore() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Retrieve this Writer's ObjectStore.
getObjectStore() - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer
Returns the ObjectStore that this ParallelPrecomputer uses.
getObjectStore(String) - Static method in class org.intermine.objectstore.ObjectStoreFactory
Return an ObjectStore configured using properties
getObjectStore() - Method in interface org.intermine.objectstore.ObjectStoreWriter
Retrieve this Writer's ObjectStore.
getObjectStore() - Method in interface org.intermine.objectstore.proxy.Lazy
Returns the ObjectStore that this lazy object will use
getObjectStore() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Returns the ObjectStore that this proxy will use
getObjectStore() - Method in class org.intermine.objectstore.proxy.ProxyReference
Returns the ObjectStore that this proxy will use
getObjectStore() - Method in class org.intermine.objectstore.query.ClobAccess
Returns the ObjectStore that this object will use to access data.
getObjectStore() - Method in class org.intermine.objectstore.query.PendingClob
Returns the ObjectStore that this object will use to access data.
getObjectStore() - Method in class org.intermine.objectstore.query.Results
Returns the ObjectStore that this Results object will use
getObjectStore() - Method in class org.intermine.objectstore.query.ResultsBatches
Returns the ObjectStore that this ResultsBatches object will use
getObjectStoreSummary() - Method in interface org.intermine.api.API
 
getObjectStoreSummary() - Method in class org.intermine.api.InterMineAPI
 
getObjectStoreWriter() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Returns the underlying ObjectStoreWriter.
getObjectStoreWriter(String) - Static method in class org.intermine.objectstore.ObjectStoreWriterFactory
Return an ObjectStoreWriter configured using properties file
getObjectStoreWriter() - Method in class org.intermine.postprocess.PostProcessor
Return the ObjectStoreWriter that was passed to the constructor.
getObjectSummaryFields() - Method in class org.intermine.web.logic.results.ReportObject
A listing of object fields as pieced together from the various ReportObject methods
getObjectTagNames(String, String, String) - Method in class org.intermine.api.profile.TagManager
Returns names of tagged tags for specified object.
getObjectTagNames(Taggable, Profile) - Method in class org.intermine.api.profile.TagManager
Returns names of tagged tags for specified object.
getObjectTags(Taggable, Profile) - Method in class org.intermine.api.profile.TagManager
Get the tags for a specific object.
getObjectTags(String, String) - Static method in class org.intermine.dwr.AjaxServices
Returns all tags by which is specified object tagged.
getOboRelations() - Method in class org.intermine.bio.ontology.OboParser
 
getOboTerms() - Method in class org.intermine.bio.ontology.OboParser
 
getOfficialName(Connection, Integer) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return the rows needed for data from the applied_protocol_data table.
getOffset() - Method in class org.intermine.objectstore.query.ClobAccess
Return the offset into the underlying clob that this object is using.
getOffset() - Method in class org.intermine.objectstore.query.PendingClob
Return the offset into the underlying clob that this object is using.
getOffset() - Method in class org.intermine.sql.precompute.LimitOffsetQuery
Getter for offset.
getOffset() - Method in class org.intermine.sql.query.Query
Gets the OFFSET number for this query.
getOffsetConstraint(Query, QueryOrderable, Object, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Create a constraint to add to the main query to deal with offset - this is based on the first element in the order by (field) and a given value (x).
getOldId() - Method in class org.intermine.web.struts.oauth2.MigrationMapping
 
getOldObject() - Method in class org.intermine.api.bag.ConvertedObjectPair
Get the objObject that was passed to the constructor.
getOldpassword() - Method in class org.intermine.web.struts.ChangePasswordForm
The old password
getOnClick() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
 
getOntology(DataConverter) - Static method in class org.intermine.bio.util.BioConverterUtil
Create and store ontology object.
getOntologyTerm() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the first value of the OntologyTerm field from the attributes of this record.
getOp() - Method in class org.intermine.objectstore.query.Constraint
Get op of constraint
getOp() - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
Returns the op of this combination.
getOp() - Method in class org.intermine.pathquery.PathConstraint
Returns the operation that this constraint performs.
getOp() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
Get a string representation of the constraint operation.
getOpened() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Returns true if disclosure is opened else false.
getOpenIdProviders(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the set of accepted Open-ID providers.
getOperands() - Method in class org.intermine.sql.query.Function
Returns the List of operands of this function.
getOperation() - Method in class org.intermine.objectstore.query.QueryExpression
Returns the operation.
getOperation() - Method in class org.intermine.objectstore.query.QueryFunction
Returns the operation of the function.
getOperation() - Method in class org.intermine.sql.query.Constraint
Returns the operation of the constraint.
getOperation() - Method in class org.intermine.sql.query.Function
Returns the operation of the function.
getOperation() - Method in class org.intermine.template.TemplateValue
 
getOperation() - Method in class org.intermine.webservice.client.template.TemplateParameter
 
getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListDifferenceService
 
getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListIntersectionService
 
getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListOperationService
Get the BagOperation that will create the list.
getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListSubtractionService
 
getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListUnionService
 
getOperationButton() - Method in class org.intermine.web.struts.SaveBagForm
 
getOperationCode() - Method in class org.intermine.api.bag.operations.BagOperation
 
getOperationCode() - Method in class org.intermine.api.bag.operations.Intersection
 
getOperationCode() - Method in class org.intermine.api.bag.operations.RelativeComplement
 
getOperationCode() - Method in class org.intermine.api.bag.operations.SymmetricDifference
 
getOperationCode() - Method in class org.intermine.api.bag.operations.Union
 
getOperator() - Method in class org.intermine.pathquery.LogicExpression.And
Override to provide text symbol for this operator.
getOperator() - Method in class org.intermine.pathquery.LogicExpression.Operator
Override to provide text symbol for this operator.
getOperator() - Method in class org.intermine.pathquery.LogicExpression.Or
Override to provide text symbol for this operator.
getOperator() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Get the operator.
getOpForIndex(Integer) - Static method in class org.intermine.metadata.ConstraintOp
Convert an index to a ConstraintOp (Only for use in webapp)
getOptimised() - Method in class org.intermine.sql.precompute.OptimiserCacheLine
Gets the optimised query (minus the LIMIT and OFFSET) from this cache line.
getOptionalParameter(String, String) - Method in class org.intermine.webservice.server.WebService
Get a parameter this service deems to be optional, or the default value.
getOptionalParameter(String) - Method in class org.intermine.webservice.server.WebService
Get a parameter this service deems to be optional, or null.
getOptions() - Method in class org.intermine.web.task.IssueTokenTask
 
getOptions() - Method in class org.intermine.web.task.KeyStoreTask
Get the options as configured for this task
getOptionsCss() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Get the name of customized options CSS
getOptionsJavascript() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Get the name of customized options javascript, by default, it is named "genomic_region_search_options_default.js"
getOptionsTileName() - Method in class org.intermine.web.logic.config.TableExportConfig
Get the optionsTileName of this TableExportConfig - ie. the tile to be inserted into the export options page for this type of export.
getOrderBy() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getOrderBy() - Method in class org.intermine.objectstore.query.Query
Gets the ORDER BY clause of this Query
getOrderBy() - Method in class org.intermine.pathquery.PathQuery
Returns the current order by list.
getOrderBy() - Method in class org.intermine.sql.query.Query
Gets the list of fields forming the ORDER BY clause of this query.
getOrderByAlias() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getOrderByField() - Method in class org.intermine.sql.precompute.PrecomputedTable
Returns the name of the order by field, if it exists.
getOrderPath() - Method in class org.intermine.pathquery.OrderElement
Returns the path of this OrderElement.
getOrganism(String) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter
The Organism item created from the taxon id passed to the constructor.
getOrganism(String) - Method in class org.intermine.bio.dataconversion.BioFileConverter
The Organism item created from the taxon id passed to the constructor.
getOrganism() - Method in class org.intermine.bio.dataconversion.EnsembSnpLoaderTask
Get and store() the Organism object to reference when creating new objects.
getOrganism(Sequence) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
Get and store() the Organism object to reference when creating new objects.
getOrganism() - Method in class org.intermine.bio.dataconversion.GFF3Converter
Return the organism Item created for this GFF3Converter from the organism abbreviation passed to the constructor.
getOrganism() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Return the organism Item set by setOrganism()
getOrganism(Sequence) - Method in class org.intermine.bio.dataconversion.UniProtFastaLoaderTask
Get and store() the Organism object to reference when creating new objects.
getOrganism() - Method in class org.intermine.bio.dataconversion.VcfLoaderTask
Get and store() the Organism object to reference when creating new objects.
getOrganism() - Method in class org.intermine.bio.web.model.GeneModelSettings
 
getOrganism() - Method in class org.intermine.bio.web.model.GenomicRegion
 
getOrganism() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
 
getOrganismConstraint() - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return some SQL that can be included in the WHERE part of query that restricts features by organism.
getOrganismConstraint() - Method in class org.intermine.bio.dataconversion.StockProcessor
Return some SQL that can be included in the WHERE part of query that restricts features by organism.
getOrganismDataByAbbreviation(String) - Method in class org.intermine.bio.util.OrganismRepository
Look up OrganismData objects by abbreviation, abbreviations are not case sensitive.
getOrganismDataByFullName(String) - Method in class org.intermine.bio.util.OrganismRepository
Look up OrganismData objects by a full name that is genus species.
getOrganismDataByGenusSpecies(String, String) - Method in class org.intermine.bio.util.OrganismRepository
Look up OrganismData objects by genus and species - both must match.
getOrganismDataByShortName(String) - Method in class org.intermine.bio.util.OrganismRepository
Look up OrganismData objects by shortName, short names are case sensitive.
getOrganismDataByTaxon(int) - Method in class org.intermine.bio.util.OrganismRepository
Look up OrganismData objects by taxon id.
getOrganismDataByTaxonInternal(int) - Method in class org.intermine.bio.util.OrganismRepository
Look up OrganismData objects by taxon id.
getOrganismDataByUniprot(String) - Static method in class org.intermine.bio.util.OrganismRepository
Look up OrganismData objects by Uniprot abbreviation, eg HUMAN or DROME.
getOrganismItem(int) - Method in class org.intermine.bio.dataconversion.BioDBConverter
The Organism item created from the taxon id passed to the constructor.
getOrganismRepository() - Static method in class org.intermine.bio.util.OrganismRepository
Return an OrganismRepository created from a properties file in the class path.
getOrganisms(ObjectStore) - Method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever
Retrieve the organisms to be updated
getOrganisms(ObjectStore, String, List<Integer>, boolean) - Static method in class org.intermine.bio.util.BioUtil
For a bag of objects, returns a list of organisms
getOrganisms(ObjectStore, String, List<Integer>, boolean, String) - Static method in class org.intermine.bio.util.BioUtil
For a bag of objects, returns a list of organisms.
getOrganisms(PathQuery, HttpSession) - Static method in class org.intermine.bio.web.logic.SequenceFeatureExportUtil
Get organism info from PathQuery
getOrganisms(PathQuery, InterMineAPI, Profile) - Static method in class org.intermine.bio.web.logic.SequenceFeatureExportUtil
 
getOrganisms() - Method in class org.intermine.bio.web.struts.GFF3ExportForm
Get the organisms set
getOrganismsToProcess() - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
Return the OrganismData objects for the organisms listed in the source configuration.
getOrganismToTaxonMap() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
 
getOrganName() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList
 
getOrgansimString() - Method in class org.intermine.bio.web.struts.BEDExportForm
 
getOrgList() - Method in class org.intermine.bio.web.model.OrganismInfo
 
getOrgName() - Method in class org.intermine.bio.web.model.ChromosomeInfo
 
getOrgName() - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint
 
getOrig() - Method in class org.intermine.dataloader.ObjectDescription
Returns the original data, as reflected in the backing database.
getOrigin() - Method in class org.intermine.api.search.OriginatingEvent
Get the web searchable involved in this event.
getOriginal() - Method in class org.intermine.sql.precompute.OptimiserCacheLine
Returns the original SQL string.
getOriginalRegion() - Method in class org.intermine.bio.web.model.GenomicRegion
Make a string of orginal region if extended
getOriginalSql() - Method in class org.intermine.sql.precompute.PrecomputedTable
Returns the original SQL text stored in the index for this PrecomputedTable
getOriginalValue() - Method in class org.intermine.web.logic.query.DisplayConstraint
 
getOrigType() - Method in class org.intermine.web.logic.query.MetadataNode
Returns the type of this node if it did not have a subclass constraint.
getOs() - Method in class org.intermine.objectstore.query.ClobAccess
Returns the ObjectStore that this object uses.
getOsb() - Method in class org.intermine.api.profile.InterMineBag
Returns the ObjectStoreBag, so that elements can be added and removed.
getOsb() - Method in class org.intermine.api.profile.InvalidBag
 
getOsb() - Method in class org.intermine.api.profile.StorableBag
Return a reference to the object store bag contained in the production database.
getOsb() - Method in class org.intermine.objectstore.query.BagConstraint
Get the ObjectStoreBag.
getOsb() - Method in class org.intermine.objectstore.query.QueryClassBag
Returns the ObjectStoreBag.
getOsName() - Method in class org.intermine.task.ConverterTask
Return the object store alias set by setOsName().
getOuterInSummary() - Method in class org.intermine.web.logic.config.FieldConfig
 
getOuterJoinGroup() - Method in class org.intermine.pathquery.Node
Returns a String describing the outer join group that this Node is in.
getOuterJoinGroup(String) - Static method in class org.intermine.pathquery.Node
Returns a String describing the outer join group that the given path string is in.
getOuterJoinGroup(String) - Method in class org.intermine.pathquery.PathQuery
Returns the outer join group that the given path is in.
getOuterJoinGroups() - Method in class org.intermine.pathquery.PathQuery
Returns the outer join groups map for this query, if the query verifies correctly.
getOuterJoinStatus(String) - Method in class org.intermine.pathquery.PathQuery
Returns the outer join status of the last part of a given path in this query.
getOuterJoinStatus() - Method in class org.intermine.pathquery.PathQuery
Returns an unmodifiable Map which is a copy of the current outer join status of this query at the time of execution of this method.
getOuterMap() - Method in class org.intermine.pathquery.PathQuery
Returns a Map from path to TRUE for all paths that are outer joined.
getOutputInfo(String) - Method in class org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient
Return the key value pairs to put in the webservice result
getOutputInfo(String) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient
Return the key value pairs to put in the webservice result
getOutputStream() - Method in class org.intermine.bio.webservice.AbstractRegionExportService
 
getOutputStream() - Method in class org.intermine.bio.webservice.BioQueryService
 
getOutro(Command) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
getOutsideOptions() - Method in class org.intermine.api.query.range.AbstractHelper
By default the OUTSIDE options are the negation of the WITHIN options, with the right and left fields swapped.
getOutwardIndirectionColumnName(CollectionDescriptor, int) - Static method in class org.intermine.sql.DatabaseUtil
Creates a column name for the "outward" key of a many-to-many collection descriptor.
getOverlapsOptions() - Method in class org.intermine.api.query.range.AbstractHelper
By default the OVERLAPS options are the same as the WITHIN options with the right and left fields swapped.
getPackageName() - Method in class org.intermine.metadata.Model
Return name of the model's package.
getPackageName() - Method in class org.intermine.objectstore.query.iql.IqlQuery
Get the package name
getPage() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the page index.
getPagedTable() - Method in class org.intermine.web.logic.query.PageTableQueryMonitor
Return the PagedTable that was passed to the constructor.
getPagedTable(HttpServletRequest, HttpSession) - Method in class org.intermine.web.struts.TableExportAction
 
getPageLink(int) - Method in class org.intermine.web.tags.table.NavigationBarTag
 
getPageName() - Method in class org.intermine.web.struts.ModifyBagForm
 
getPageName() - Method in class org.intermine.web.struts.ModifyTemplateForm
 
getPageSize() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the page size of the current page
getPageSize() - Method in class org.intermine.web.struts.ChangeTableSizeForm
Get the page size
getPageSize() - Method in class org.intermine.web.tags.table.NavigationBarTag
 
getParam() - Method in class org.intermine.objectstore.query.QueryFunction
Returns the QueryEvaluable of the function.
getParam2() - Method in class org.intermine.objectstore.query.QueryFunction
Returns the second evaluable, where these is one.
getParameter(String) - Method in interface org.intermine.webservice.client.core.Request
Use only if you are sure, that the parameter has only one value else use getParameterValues method.
getParameter(String) - Method in class org.intermine.webservice.client.core.RequestImpl
Use only if you are sure, that the parameter has only one value else use getParameterValues method.
getParameter(String) - Method in class org.intermine.webservice.server.jbrowse.Command
 
getParameter(String, String) - Method in class org.intermine.webservice.server.jbrowse.Command
 
getParameterJson() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the parameters for this displayer as a JSONObject
getParameterMap() - Method in interface org.intermine.webservice.client.core.Request
Returns all parameters as an unmodifiable map.
getParameterMap() - Method in class org.intermine.webservice.client.core.RequestImpl
Returns all parameters as an unmodifiable map.
getParameterName() - Method in class org.intermine.web.logic.template.ConstraintInput
 
getParameterNames() - Method in interface org.intermine.webservice.client.core.Request
 
getParameterNames() - Method in class org.intermine.webservice.client.core.RequestImpl
getParameters() - Method in class org.intermine.objectstore.query.iql.IqlQuery
Get the parameters
getParameters() - Method in class org.intermine.web.util.AttributeLinkURL
 
getParameterString() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
A JSON string representing custom parameters for this displayer.
getParameterValues(String) - Method in interface org.intermine.webservice.client.core.Request
 
getParameterValues(String) - Method in class org.intermine.webservice.client.core.RequestImpl
getParams() - Method in class org.intermine.web.logic.config.Displayer
Return the parameters stored in this Displayer.
getParent() - Method in class org.intermine.objectstore.query.OverlapRange
Returns the parent parameter.
getParent() - Method in class org.intermine.pathquery.Node
Get the parent node.
getParent() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns a new DisplayPath that represents the parent path, or null if this path is just a root class.
getParentId() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
Get parentId value
getParents() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the list of the Parent field from the attributes of this record.
getParentTermId() - Method in class org.intermine.bio.ontology.OboRelation
 
getParentType() - Method in class org.intermine.pathquery.Node
Type of parent node.
getParentType() - Method in class org.intermine.web.logic.results.InlineResultsTable
Get the parent's type
getPartialString(List<String>) - Method in class org.intermine.pathquery.LogicExpression
Produce an expression for this branch of the tree displaying only the children containing the variable in input
getParticipant() - Method in class org.intermine.webservice.server.complexes.ExportService.FeatureHolder
 
getParts() - Method in class org.intermine.webservice.client.core.MultiPartRequest
 
getPassword() - Method in class org.intermine.api.profile.Profile
Get the value of password
getPassword(String) - Method in class org.intermine.api.profile.ProfileManager
Get a user's password A check should be made prior to this call to ensure a Profile exists
getPassword() - Method in class org.intermine.sql.Database
Gets the password for this Database
getPassword() - Method in class org.intermine.web.struts.CreateAccountForm
 
getPassword() - Method in class org.intermine.web.struts.LoginForm
Gets the value of password
getPassword() - Method in class org.intermine.webservice.server.WebServiceInput
 
getPassword2() - Method in class org.intermine.web.struts.CreateAccountForm
 
getPath() - Method in class org.intermine.api.results.Column
Get the Path set by setPath().
getPath() - Method in interface org.intermine.api.results.ResultCell
 
getPath() - Method in class org.intermine.api.results.ResultElement
 
getPath() - Method in class org.intermine.pathquery.PathConstraint
Returns the path that this constraint is attached to.
getPath() - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart
The path that should be in the title, with style removed.
getPath() - Method in class org.intermine.web.logic.config.InlineListConfig
 
getPath() - Method in class org.intermine.web.logic.query.DisplayConstraint
Get a representation of the path that is being constraint.
getPath() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Return the underlying path object.
getPath() - Method in class org.intermine.web.logic.results.InlineList
 
getPath() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of path
getPath() - Method in class org.intermine.webservice.server.core.TableCell
 
getPathConstraint() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
Returns the pathConstraint based on the enrichmentIdentifier will be applied on the pathQUery
getPathConstraints() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getPathConstraintsForView() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getPathId() - Method in class org.intermine.web.logic.template.ConstraintInput
 
getPathId() - Method in class org.intermine.webservice.client.template.TemplateParameter
 
getPathQuery() - Method in class org.intermine.api.profile.SavedQuery
Get the saved PathQuery.
getPathQuery() - Method in class org.intermine.api.results.WebResults
 
getPathQuery() - Method in interface org.intermine.api.results.WebTable
Get the PathQuery associated with this WebTable
getPathQuery() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
 
getPathQuery() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
getPathQuery() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
Returns the pathquery based on the views set in config file and the bag constraint Executed when the user selects any item in the matches column in the enrichment widget.
getPathQuery() - Method in class org.intermine.web.logic.widget.GraphWidget
Returns the pathquery based on the views set in config file and the bag constraint.
getPathQuery() - Method in class org.intermine.web.logic.widget.HTMLWidget
 
getPathQuery() - Method in class org.intermine.web.logic.widget.TableWidget
 
getPathQuery() - Method in class org.intermine.web.logic.widget.Widget
Return the PathQuery generated dynamically by the attribute views in the configuration file
getPathQueryExecutor(Profile) - Method in interface org.intermine.api.API
 
getPathQueryExecutor() - Method in class org.intermine.api.InterMineAPI
 
getPathQueryExecutor(Profile) - Method in class org.intermine.api.InterMineAPI
 
getPathQueryExecutor() - Static method in class org.intermine.api.query.PathQueryAPI
Returns a PathQueryExecutor, using properties.
getPathQueryForMatches() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
Returns the pathquery based on the startClassDisplay, constraintsForView set in config file and the bag constraint Executed when the user click on the matches column in the enrichment widget.
getPathQueryViews(String[]) - Static method in class org.intermine.bio.webservice.BioQueryService
Parse path query views from request parameter "view" comma-separated
getPathsString() - Method in class org.intermine.web.struts.TableExportForm
Get the paths string in the format: "Class.field Class.field2 Class.ref.field"
getPathString() - Method in class org.intermine.pathquery.Node
Gets the String value of pathString of this node (eg.
getPathString() - Method in exception org.intermine.pathquery.PathException
Return the path String that was passed to the constructor.
getPathString() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns the full path string for this path.
getPathString() - Method in class org.intermine.web.logic.results.ReportObjectField
Get a path string to fetch field descriptions
getPathStrings() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
Comma separated list of path strings to appear in the widget, ie Employee.firstName, Employee.lastName
getPathToBagQueryResult() - Method in class org.intermine.api.results.WebResults
Returns the pathToBagQueryResult Map.
getPathToBagQueryResult() - Method in interface org.intermine.api.results.WebTable
Returns the pathToBagQueryResult Map.
getPathToIndex() - Method in class org.intermine.api.results.WebResults
Create a map from string paths to index of QueryNodes in the ObjectStore query
getPathToQueryNode() - Method in class org.intermine.api.results.WebResults
Returns the pathToQueryNode Map.
getPathUpdated(String, Map<String, String>, Map<String, String>) - Method in class org.intermine.api.profile.PathQueryUpdate
Update the path given in input with the renamed classes and fields
getPathWithoutSubClass(Model, String) - Static method in class org.intermine.web.logic.widget.config.WidgetConfigUtil
 
getPerlWSModuleVer() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
getPermanentBaseURL() - Method in class org.intermine.web.util.URLGenerator
Generates base url.
getPermission(String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
Get the level of permission granted by an access token.
getPermission(PermanentToken, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
 
getPermission(String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
Authenticate a user using username/password credentials.
getPermission() - Method in class org.intermine.webservice.server.WebService
Return the permission object representing the authorisation state of the request.
getPhase() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the phase field of this record.
getPlacement() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the data category name under which this displayer should appear.
getPlatform() - Method in class org.intermine.sql.Database
Gets the platform of this Database
getPoints() - Method in class org.intermine.web.search.KeywordSearchResult
return points
getPopularTemplatesByAspect(String, Integer) - Method in class org.intermine.api.template.TemplateManager
Return the template list for a particular aspect given in input, ordered by rank descendant
getPopularTemplatesByAspect(String, Integer, String, String) - Method in class org.intermine.api.template.TemplateManager
Return the template list for a particular aspect, ordered by rank descendant for the user/sessionid specified in the input
getPopulatedTemplate(TemplateQuery, Map<String, List<TemplateValue>>) - Static method in class org.intermine.api.template.TemplatePopulator
Given a template and a map of values for editable constraints on each editable node create a copy of the template query with the values filled in.
getPopulationBagName() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
Get the bag's name for reference population
getPopulationInfo() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
Return a population info instance contanining the population size, N (In our example this is the total number of companies, or possibly the total number of companies that have at least one Department) and the average length of the genes in the whole population.
getPopulationInfo() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
 
getPopulationQuery(boolean) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr
 
getPossibleValues(ApiTemplate, String) - Method in class org.intermine.api.template.TemplateSummariser
Returns the possible values that a particular path in a template query can take, for dropdowns on template forms.
getPossibleValues(ApiTemplate) - Method in class org.intermine.api.template.TemplateSummariser
Returns a Map of the possible values for editable nodes on a template query.
getPossibleValues() - Method in class org.intermine.web.logic.query.DisplayConstraint
Values to populate a dropdown for the path if possible values are available.
getPostProcesses() - Method in class org.intermine.task.project.Project
Return a Map from post-process name to PostProcess objects
getPrecomputedSummarisedInfo(Profile, HttpSession, HttpServletRequest) - Static method in class org.intermine.web.struts.MyMineController
Retrieve the information about precomputed and summarised templates for the given profile, and store it into the request
getPrecomputedTables() - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Get all the precomputed tables in the underlying database.
getPrecomputeQuery(TemplateQuery, List) - Static method in class org.intermine.api.template.TemplatePrecomputeHelper
Get an ObjectStore query to precompute this template - remove editable constraints and add fields to select list if necessary.
getPrecomputeQuery(TemplateQuery, List<? super QueryNode>, String) - Static method in class org.intermine.api.template.TemplatePrecomputeHelper
Get an ObjectStore query to precompute this template - remove editable constraints and add fields to select list if necessary.
getPrecomputeQuery(TemplateQuery, List<? super QueryNode>, String, InterMineAPI) - Static method in class org.intermine.api.template.TemplatePrecomputeHelper
Get an ObjectStore query to precompute this template - remove editable constraints and add fields to select list if necessary.
getPrecomputer(ObjectStoreInterMineImpl) - Method in class org.intermine.task.PrecomputeTask
Create a ParallelPrecomputer.
getPrecomputeTemplateQueries() - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Get the super user's public templates
getPreDefaultBagQueries(String) - Method in class org.intermine.api.bag.BagQueryConfig
Return a List of BagQuerys for the given type that should be run before the default query
getPreferences(Profile) - Method in class org.intermine.api.profile.PreferencesManager
 
getPreferences() - Method in class org.intermine.api.profile.Profile
Get the object representing the preferences of this user.
getPreferences(Profile) - Method in class org.intermine.api.profile.ProfileManager
Get the preferences for a profile.
getPrefix() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
 
getPrefix() - Method in class org.intermine.pathquery.Node
Gets the value of prefix
getPrefix() - Method in class org.intermine.pathquery.Path
Return a Path object that represents the prefix of this path, ie this Path without the last element.
getPrefix() - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart
A prefix that may be an HTML tag to appear before this part in the title.
getPrefix() - Method in class org.intermine.web.logic.results.InlineList
 
getPrefixes() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
used for testing
getPreviousLink(int) - Method in class org.intermine.web.tags.table.NavigationBarTag
 
getPrimaryAccession() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getPrimaryId() - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary
 
getPrimaryIdentifier() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getPrimaryKeys(ClassDescriptor, Source, ObjectStore) - Static method in class org.intermine.dataloader.DataLoaderHelper
Return a Set of PrimaryKeys relevant to a given Source for a ClassDescriptor.
getPrimaryKeys(ClassDescriptor) - Static method in class org.intermine.metadata.PrimaryKeyUtil
Retrieve a map from key name to PrimaryKey object.
getPrintWriter() - Method in class org.intermine.bio.webservice.AbstractRegionExportService
 
getPrintWriter() - Method in class org.intermine.bio.webservice.BioQueryService
 
getPrintWriterForClient(HttpServletRequest, OutputStream) - Static method in class org.intermine.web.logic.export.http.HttpExportUtil
 
getPriorities(Class<? extends FastPathObject>, String) - Method in class org.intermine.dataloader.PriorityConfig
Returns a List of data source names representing the priority for a given class and fieldname pair.
getProblems() - Method in exception org.intermine.api.query.codegen.InvalidQueryException
 
getProblems() - Method in class org.intermine.metadata.Model
Return a list of problems with the model or an empty list.
getProcessingInstruction() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
getProcessingInstruction() - Method in class org.intermine.webservice.server.output.XMLFormatter
 
getProcessor() - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService
 
getProcessor() - Method in class org.intermine.webservice.server.widget.GraphService
 
getProcessor() - Method in class org.intermine.webservice.server.widget.TableWidgetService
 
getProcessor() - Method in class org.intermine.webservice.server.widget.WidgetService
 
getProductionObjectStore() - Method in class org.intermine.api.profile.ProfileManager
Return the ObjectStore that was passed to the constructor.
getProfile() - Method in class org.intermine.api.bag.operations.BagOperation
 
getProfile() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
 
getProfile(String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
Get a user's Profile using a username, password and the classKeys.
getProfile(String, String) - Method in class org.intermine.api.profile.ProfileManager
Get a user's Profile using a username and password.
getProfile(String) - Method in class org.intermine.api.profile.ProfileManager
Get a user's Profile using a username
getProfile(int) - Method in class org.intermine.api.profile.ProfileManager
Get a user's Profile using an ID
getProfile(String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
Get a user's Profile using a username
getProfile() - Static method in class org.intermine.api.query.PathQueryAPI
Returns the superuser Profile.
getProfile() - Method in class org.intermine.api.search.SearchRepository
Get the profile that this repository belongs to.
getProfile(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Returns user profile saved in session.
getProfile() - Method in class org.intermine.webservice.server.user.DeletionToken
 
getProfileId() - Method in class org.intermine.api.profile.StorableBag
 
getProfileManager() - Method in interface org.intermine.api.API
 
getProfileManager() - Method in class org.intermine.api.InterMineAPI
 
getProfileManager() - Method in class org.intermine.api.profile.Profile
Return the ProfileManager that was passed to the constructor.
getProfileManager() - Static method in class org.intermine.api.query.PathQueryAPI
Returns the ProfileManager configured in webapp.userprofile.os.alias.
getProfileObjectStoreWriter() - Method in class org.intermine.api.profile.ProfileManager
Return the userprofile ObjectStoreWriter that was passed to the constructor.
getProfileUserName(int) - Method in class org.intermine.api.profile.ProfileManager
Return the name of the user with the given internal DB id.
getProfileUserNames() - Method in class org.intermine.api.profile.ProfileManager
Return a List of the usernames in all of the stored profiles.
getProjectBaseDir(String) - Method in class org.intermine.task.Dependencies
Given a project name, returning the corresponding project directory.
getProjects(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return the project name.
getProjectTitle() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
getProperties() - Static method in class org.intermine.api.query.PathQueryAPI
Returns the properties accessible for this system.
getProperties() - Method in class org.intermine.task.project.Project
Return a list of UserProperty objects for the Project.
getProperties() - Static method in class org.intermine.util.PropertiesUtil
Returns all InterMine properties
getProperties() - Method in class org.intermine.webservice.client.results.Item
Return a view of the properties in this row.
getPropertiesFileName(String) - Static method in class org.intermine.task.PrecomputeTask
Return the name of the properties file we will read.
getPropertiesOrigins(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Gets the origins map from the servlet context.
getPropertiesStartingWith(String, Properties) - Static method in class org.intermine.metadata.Util
Returns all Properties in props that begin with str
getPropertiesStartingWith(String, Properties) - Static method in class org.intermine.util.PropertiesUtil
Returns all Properties in props that begin with str
getPropertiesStartingWith(String) - Static method in class org.intermine.util.PropertiesUtil
Returns all global Properties that begin with str
getProperty(String, String) - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
Get a configured property for which an accessor does not exist.
getProperty() - Method in class org.intermine.web.logic.query.DisplayConstraint.DisplayConstraintOption
Get the constraint index to be put in form when this op is selected.
getProperty(String) - Method in class org.intermine.webservice.server.jbrowse.util.NameSpacedProperties
 
getProperty(String, String) - Method in class org.intermine.webservice.server.jbrowse.util.NameSpacedProperties
 
getProperty(String) - Method in class org.intermine.webservice.server.WebService
Get a configuration property by name.
getPropertyDescriptors() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getPropertyDescriptors() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getPropertyName() - Method in class org.intermine.web.struts.EditPropertiesForm
 
getPropertyValue() - Method in class org.intermine.web.struts.EditPropertiesForm
 
getProteinForSequence(ObjectStore, Sequence) - Static method in class org.intermine.bio.web.export.ResidueFieldExporter
Find the Protein that references the given Sequence.
getProteinNames() - Method in class org.intermine.bio.dataconversion.UniprotEntry
if an isoform has two ID tags, then the first one is used and the second one is added as a synonym
getProtocolAttributes(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return the rows needed for protocols from the attribute table.
getProtocols(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return the rows needed from the protocol table.
getProvider() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
 
getProxyGetter() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the proxyGetter Method.
getProxyGetter(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the Method object that is the proxyGetter for the field name
getProxySetter() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the proxySetter Method.
getProxySetter(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the Method object that is the proxySetter for the field name
getPublicationReferenceList() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Return a ReferenceList containing the Publication Items ids set by addPublication()
getPublications(ObjectStore) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
Retrieve the publications to be updated
getPublicId() - Method in class org.intermine.webservice.server.lists.ListsServiceInput
Returns id of object.
getPublicTagNames(ClassDescriptor) - Method in class org.intermine.api.profile.TagManager
Get all the tags that all users have access to.
getPublicTagNames(Taggable) - Method in class org.intermine.api.profile.TagManager
Get all the tags that all users have access to.
getPublicTagNames(String, String) - Method in class org.intermine.api.profile.TagManager
Get the tags for an object that are visible to all users.
getPubRefId(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getPubResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return the interesting rows from the pub table.
getPubs() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getPValue() - Method in class org.intermine.web.struts.WidgetForm
 
getPValues() - Method in class org.intermine.web.logic.widget.EnrichmentResults
Get the probability of enrichment for each attribute value found in the sample.
getQcb() - Method in class org.intermine.objectstore.query.QueryCollectionReference
Gets the QueryClassBag of this QueryReference.
getQcObject() - Method in class org.intermine.objectstore.query.QueryCollectionReference
Gets the InterMineObject of this QueryReference.
getQcType() - Method in class org.intermine.objectstore.query.QueryCollectionReference
Returns the type of the queryclass of this reference
getQcType() - Method in class org.intermine.objectstore.query.QueryReference
Returns the type of the queryclass of this reference
getQope() - Method in class org.intermine.objectstore.query.PathExpressionField
Returns the QueryObjectPathExpression.
getQualifiedType() - Method in class org.intermine.api.profile.InterMineBag
Get the fully qualified type of this bag
getQualifiedTypeName(String) - Method in class org.intermine.metadata.Model
Return the qualified name of the given unqualified class name.
getQueried(String) - Method in class org.intermine.dataloader.EquivalentObjectHints
Returns a Set of values that have been tested for a particular class and fieldname.
getQueries() - Method in class org.intermine.sql.precompute.BestQueryStorer
Gets the set of queries added to this object
getQuery(Collection<String>, String) - Method in class org.intermine.api.bag.BagQuery
Return the Query that was passed to the constructor.
getQuery() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
getQuery(String) - Method in class org.intermine.api.query.MemoryQueryStore
 
getQuery(String) - Method in interface org.intermine.api.query.QueryStore
 
getQuery() - Method in class org.intermine.api.results.ExportResultsIterator
 
getQuery() - Method in class org.intermine.bio.webservice.BioQueryService
Return the query specified in the request, shorn of all duplicate classes in the view.
getQuery() - Method in class org.intermine.bio.webservice.FastaListService
 
getQuery() - Method in class org.intermine.bio.webservice.FastaQueryService
Make the path-query to run, and check it has the right number of columns.
getQuery() - Method in class org.intermine.bio.webservice.GFF3ListService
 
getQuery() - Method in interface org.intermine.objectstore.proxy.LazyCollection
Returns the Query used by this LazyCollection
getQuery() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Returns the Query used by this LazyCollection
getQuery(Collection<? extends InterMineObject>) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the Query that will fetch the data represented by this object, given a Collection of objects to fetch it for.
getQuery(Collection<Integer>, boolean) - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Returns the Query that will fetch the data represented by this object, given a Collection of objects to fetch it for.
getQuery() - Method in class org.intermine.objectstore.query.Results
Get the Query that produced this Results object.
getQuery() - Method in class org.intermine.objectstore.query.ResultsBatches
Get the Query that produced this ResultsBatches object.
getQuery() - Method in class org.intermine.objectstore.query.SubqueryConstraint
Get the query.
getQuery() - Method in class org.intermine.objectstore.query.SubqueryExistsConstraint
Get the query.
getQuery() - Method in class org.intermine.objectstore.querygen.QueryGenUtil.QueryAndClass
Returns the query.
getQuery() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
Returns the Query of this Candidate, converting from a String if necessary.
getQuery() - Method in class org.intermine.sql.precompute.LimitOffsetQuery
Getter for the stripped query.
getQuery() - Method in class org.intermine.sql.precompute.PrecomputedTable
Gets the Query that is materialised in this PrecomputedTable
getQuery() - Method in class org.intermine.sql.query.SubQuery
Returns the query contained in the subquery.
getQuery() - Method in class org.intermine.web.logic.session.QueryCountQueryMonitor
Return the Query that was passed to the constructor.
getQuery(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Returns the PathQuery on the session.
getQuery(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods
Returns the PathQuery on the session.
getQuery(String, List<String>) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr
Returns the relevant query.
getQuery(boolean, List<String>) - Method in class org.intermine.web.logic.widget.TableWidgetLdr
 
getQuery() - Method in class org.intermine.web.struts.QueryForm
 
getQuery(HttpServletRequest) - Method in class org.intermine.webservice.server.query.QueryToListService
Get the pathquery to use for this request.
getQuery(PathQuery, Profile) - Method in class org.intermine.webservice.server.query.QueryToListService
Get the Objectstore Query to run to generate the list.
getQuery() - Method in class org.intermine.webservice.server.query.result.PathQueryBuilder
Returns parsed PathQuery.
getQuery() - Method in class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj
For the purposes of exporting into JSON objects the view must be: Ordered by length, such that Company.departments.name precedes Company.departments.employees.name Be constituted so that every class has an attribute on it, root class included, and every reference along the way.
getQuery(HttpServletRequest) - Method in class org.intermine.webservice.server.template.TemplateToListService
 
getQueryBuilder() - Method in class org.intermine.web.struts.ImportQueriesForm
Get the queryBuilder field.
getQueryBuilder(String) - Method in class org.intermine.webservice.server.query.AbstractQueryService
Get a path-query builder.
getQueryClass() - Method in class org.intermine.objectstore.query.ContainsConstraint
Returns the QueryClass of the constraint.
getQueryClass() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the QueryClass of which the field is a member.
getQueryClass() - Method in class org.intermine.objectstore.query.QueryForeignKey
Gets the QueryClass of which this reference is an member.
getQueryClass() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Returns the QueryClass of which the field is a member.
getQueryClass() - Method in interface org.intermine.objectstore.query.QueryPathExpressionWithSelect
Returns the QueryClass of which the field is a member.
getQueryClass() - Method in class org.intermine.objectstore.query.QueryReference
Gets the QueryClass of which this reference is an member.
getQueryClass() - Method in class org.intermine.objectstore.query.SubqueryConstraint
Get the QueryClass the query is compare with
getQueryDesc() - Method in class org.intermine.api.bag.BagQueryResult.IssueResult
 
getQueryEvaluable() - Method in class org.intermine.objectstore.query.SubqueryConstraint
Get the QueryEvaluable the query is compared with
getQueryFields(QueryEvaluable) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Descends into QueryExpression and QueryFunction objects to find all instances of QueryField.
getQueryForWildcards(Collection<String>, String) - Method in class org.intermine.api.bag.BagQuery
Return a Query to fetch bag contents for wildcards.
getQueryInfo(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor
Retrieve an entry from the infoCache.
getQueryMap() - Method in class org.intermine.web.struts.ImportQueriesForm
Return a Map from query name to Query object.
getQueryMap(BagManager, Profile) - Method in class org.intermine.web.struts.TemplatesImportForm
Return a Map from template name to Template object.
getQueryName() - Method in class org.intermine.web.struts.SaveQueryForm
Get the query name
getQueryNode() - Method in class org.intermine.objectstore.query.BagConstraint
Get the QueryNode.
getQueryOrderable() - Method in class org.intermine.objectstore.query.OrderDescending
Return the encapsulated QueryOrderable.
getQueryPaths(PathQuery) - Method in class org.intermine.bio.webservice.BioQueryService
Parse view strings to Path objects
getQueryService() - Method in class org.intermine.webservice.client.core.ServiceFactory
Return a new QueryService for getting query results from.
getQueryStore() - Method in class org.intermine.api.InterMineAPI
 
getQueryString() - Method in class org.intermine.objectstore.query.iql.IqlQuery
Get the query String NOTE: this will be unvalidated
getQueryString() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
Returns the String query of this Candidate, converting from Query if necessary.
getQueryTime() - Method in class org.intermine.objectstore.intermine.ExtraQueryTime
Returns the total amount of time spent in extra queries, in milliseconds.
getQueryToExecute() - Method in class org.intermine.pathquery.PathQuery
Get the PathQuery that should be executed.
getQueryToExecute() - Method in class org.intermine.template.TemplateQuery
Fetch the PathQuery to execute for this template.
getQueryTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices
 
getQueryTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices
 
getQueryWithDefaultView(String, Model, WebConfig, String) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
Used for making a query for a reference or collection.
getQueryXml() - Method in class org.intermine.webservice.server.query.QueryRequestParser
Get query XML from a request.
getRangeConstraint() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Get the range constraint value.
getRangeLabel() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
Get the value of rangeLabel
getRangeOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
getRangeQueryOps() - Method in class org.intermine.web.logic.query.DisplayConstraint
Returns the set of operators valid for range constraints.
getRanges() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
getRangeSetOp() - Method in class org.intermine.api.query.range.ConstraintOptions
 
getRank(TemplateManager) - Method in class org.intermine.api.tracker.TemplateTracker
Return the rank for each public template.It represents a relationship between the templates executions; a template with rank 1 has been executed more than a template with rank 2.
getRank(TemplateManager) - Method in class org.intermine.api.tracker.TrackerDelegate
Return the rank associated to the templates
getRatDiseases(String) - Static method in class org.intermine.dwr.AjaxServices
Return list of disease ontology terms associated with list of provided rat genes.
getRatIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a rat id resolver
getRatIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a rat id resolver
getRatIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a rat id resolver
getRawOutput() - Method in class org.intermine.webservice.server.WebService
Get access to the underlying print-writer.
getReader(Set<Integer>) - Method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever
Obtain the pubmed esummary information for the organisms
getReader(Integer) - Static method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever
 
getReader(Set<Integer>) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
Obtain the pubmed esummary information for the publications
getReader() - Method in class org.intermine.webservice.client.results.ResultSet
Get a reader over the data, for reading line-by-line.
getReader(HttpServletRequest) - Method in class org.intermine.webservice.server.lists.ListUploadService
Get the reader for the identifiers uploaded with this request.
getReason() - Method in exception org.intermine.webservice.client.exceptions.ResultException
Get the reason for this error.
getReference() - Method in class org.intermine.objectstore.query.ContainsConstraint
Returns the QueryReference of the constraint.
getReference(String) - Method in class org.intermine.webservice.client.results.Item
Get in Item representing the record referenced by a reference field.
getReference(String) - Method in class org.intermine.xml.full.Item
Get a named reference.
getReferencedClassDescriptor() - Method in class org.intermine.metadata.ReferenceDescriptor
Returns a ClassDescriptor for the object referenced by this field.
getReferencedClassName() - Method in class org.intermine.metadata.ReferenceDescriptor
Returns the class name of the object referenced by this field.
getReferenceDescriptorByName(String) - Method in class org.intermine.metadata.ClassDescriptor
Gets a ReferenceDescriptor for a field of the given name.
getReferenceDescriptorByName(String, boolean) - Method in class org.intermine.metadata.ClassDescriptor
Gets a ReferenceDescriptor for a field of the given name.
getReferenceDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets the descriptors for the external object references in this class.
getReferenceLists() - Method in class org.intermine.webservice.server.lists.ListInput
 
getReferenceName() - Method in class org.intermine.bio.chado.config.CreateCollectionAction
Return the referenceName that was passed to the constructor.
getReferences() - Method in class org.intermine.objectstore.intermine.DatabaseSchema.Fields
Returns the Set of references
getReferences() - Method in class org.intermine.xml.full.Item
Get all the references.
getRefId() - Method in class org.intermine.xml.full.Reference
Get the refId of this field
getRefIds() - Method in class org.intermine.xml.full.ReferenceList
Get the references in this collection.
getRefsAndCollections() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
 
getRefsAndCollections() - Method in class org.intermine.web.logic.results.ReportObject
Get all the reference and collection fields and values for this object
getRegions() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
 
getRegionStringFromPathQuery(PathQuery, InterMineAPI, Profile) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner
query chromosome locations by a ready-to-use pathquery, return region string as chr:start..end
getRegionStringFromSequenceFeatureList(Collection<SequenceFeature>, InterMineAPI, Profile) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner
query chromosome locations by a list of sequence features, return region string as chr:start..end
getRelationship() - Method in class org.intermine.bio.ontology.OboRelation
 
getRelease() - Static method in class org.intermine.web.filters.ReleaseEtagFilter
 
getRelease() - Method in class org.intermine.webservice.client.core.Service
 
getReleaseVersion() - Method in class org.intermine.api.mines.LocalMine
 
getReleaseVersion() - Method in interface org.intermine.api.mines.Mine
 
getReleaseVersion() - Method in class org.intermine.api.mines.RemoteMine
 
getRelevantConstraints() - Method in class org.intermine.pathquery.PathQuery
 
getRelevantConstraints() - Method in class org.intermine.template.TemplateQuery
 
getReliability() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions
 
getRenamedBags() - Method in class org.intermine.web.logic.profile.ProfileMergeIssues
Get the mapping from old to new names.
getRenamedClasses() - Method in class org.intermine.api.profile.ModelUpdate
Return a map containing the couple previous class and new class
getRenamedFields() - Method in class org.intermine.api.profile.ModelUpdate
Return a map containing the couple previousClass.previuosField and new field
getRenamedTemplates() - Method in class org.intermine.web.logic.profile.ProfileMergeIssues
Get the names of all the templates that failed.
getReplacedFieldExprs() - Method in class org.intermine.web.displayer.ReportDisplayer
Get a list of field names and paths that should be replaced by this displayer - i.e. this displayer should be shown instead of other fields.
getReplacedFieldExprs() - Method in class org.intermine.web.logic.results.ReportObject
Get fields and paths that are replaced by custom report displayers and should not be shown in the report page.
getReplacedFieldNames() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the names of fields this displayer replaces.
getReplacesFields() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the comma separated list of field names that should not be displayed on the report page when this displayer is used.
getReportDisplayer(String) - Method in class org.intermine.web.logic.results.ReportObject
Give us a displayer by a specific name, called by AjaxServices
getReportDisplayerByName(String, String) - Method in class org.intermine.web.displayer.DisplayerManager
Get a specific ReportDisplayer by its name for a given ReportObject type
getReportDisplayerConfigs() - Method in class org.intermine.web.logic.config.WebConfig
Fetch config for the report page displayers.
getReportDisplayers() - Method in class org.intermine.web.logic.results.ReportObject
Get a map from placement (header, summary or a data category) to custom report displayers for that placement.
getReportDisplayersForType(String) - Method in class org.intermine.web.displayer.DisplayerManager
Get a map from placement string (a data category or summary) to displayers for the given type.
getReportObject(HttpSession, String) - Method in class org.intermine.web.struts.ModifyDetails
Get a ReportObject from the session given the object id as a string.
getReportObjects(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Return the ReportObjects Map from the session or create and return it if it doesn't exist.
getReportPageTemplatesForAspect(String, Set<String>) - Method in class org.intermine.api.template.TemplateManager
Get a list of template queries that should appear on report pages for the given type under the specified aspect.
getRequest() - Static method in class org.intermine.objectstore.query.PrefetchManager
Returns a request for a thread to service.
getRequestFileName() - Method in class org.intermine.webservice.server.WebService
If the request has a filename parameter then use that for the fileName, otherwise use the default fileName
getRequiredParameter(String) - Method in class org.intermine.webservice.server.WebService
Get a parameter this service deems to be required.
getResponseBodyAsStream() - Method in class org.intermine.webservice.client.util.HttpConnection
 
getResponseBodyAsString() - Method in class org.intermine.webservice.client.util.HttpConnection
Return the response body, ensuring that the connection is closed upon completion.
getResponseCode() - Method in class org.intermine.webservice.client.util.HttpConnection
 
getResponseHeader(String) - Method in class org.intermine.webservice.client.util.HttpConnection
 
getResponseStream() - Method in class org.intermine.webservice.client.util.HttpConnection
 
getResponseTable(Request) - Method in class org.intermine.webservice.client.services.AbstractQueryService
Performs the actual remote request and fetches the results.
getResponseType() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
 
getResponseType() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
 
getResponseType() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
 
getResult() - Method in interface org.intermine.api.idresolution.Job
 
getResult() - Method in class org.intermine.api.idresolution.ResolutionJob
 
getResult() - Method in class org.intermine.api.idresolution.UpgradeJob
 
getResultElementRows() - Method in class org.intermine.web.logic.results.InlineResultsTable
Main method used from report to resolve a tablefull of ResultElements
getResultElements(int) - Method in class org.intermine.api.results.WebResults
Return a List containing a ResultElement object for each element in the given row.
getResultElements(int) - Method in interface org.intermine.api.results.WebTable
Return a List containing a ResultElement object for each element given in the given row.
getResultRows(PagedTable, HttpServletRequest) - Method in class org.intermine.web.logic.export.http.HttpExporterBase
 
getResults() - Method in class org.intermine.api.bag.BagQueryResult.IssueResult
 
getResults() - Method in class org.intermine.model.testmodel.web.widget.AgeGroupLdr
 
getResults() - Method in class org.intermine.model.testmodel.web.widget.AgeSalaryLdr
 
getResults() - Method in class org.intermine.model.testmodel.web.widget.AgeSeniorityLdr
 
getResults() - Method in class org.intermine.model.testmodel.web.widget.CompanyDistLdr
 
getResults() - Method in class org.intermine.model.testmodel.web.widget.FullTimeLdr
 
getResults() - Method in interface org.intermine.web.logic.widget.DataSetLdr
Get the Results object
getResults() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
 
getResults() - Method in class org.intermine.web.logic.widget.GraphWidget
 
getResults() - Method in class org.intermine.web.logic.widget.GraphWidgetLoader
 
getResults() - Method in class org.intermine.web.logic.widget.HTMLWidget
 
getResults() - Method in class org.intermine.web.logic.widget.TableWidget
 
getResults() - Method in class org.intermine.web.logic.widget.Widget
Return the result that represents the data from this widget.
getResults() - Method in class org.intermine.webservice.client.results.JSONResult
 
getResults(PathQuery, Page) - Method in class org.intermine.webservice.client.services.QueryService
 
getResults(String, Page) - Method in class org.intermine.webservice.client.services.QueryService
Returns a specific set of the results of the specified PathQuery.
getResults(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService
Returns a set of the results for the given template template with the given parameters, defined by the index of the first result you want back, and the maximum page size.
getResults(TemplateQuery, Page) - Method in class org.intermine.webservice.client.services.TemplateService
 
getResults() - Method in class org.intermine.webservice.server.output.MemoryOutput
Returns results added to output
getResultsAsList() - Method in class org.intermine.web.logic.results.InlineResultsTable
 
getResultsBatches() - Method in class org.intermine.objectstore.query.Results
Returns the underlying ResultsBatches object that this object is using, in order to create more Results objects (with different settings) from it.
getResultsCount() - Method in class org.intermine.webservice.server.output.MemoryOutput
}
getResultsCount() - Method in class org.intermine.webservice.server.output.Output
 
getResultsCount() - Method in class org.intermine.webservice.server.output.StreamedOutput
getResultsCss() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Get the name of customized results CSS
getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONDataTableRowResultProcessor
 
getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONObjResultProcessor
 
getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONResultProcessor
The method a processor must implement to produce a results iterator.
getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONRowResultProcessor
 
getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONSummaryProcessor
 
getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONTableResultProcessor
 
getResultsJavascript() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Get the name of customized results javascript
getResultsKey() - Method in class org.intermine.webservice.server.branding.BrandingService
 
getResultsKey() - Method in class org.intermine.webservice.server.core.JSONService
 
getResultsKey() - Method in class org.intermine.webservice.server.data.DataService
 
getResultsKey() - Method in class org.intermine.webservice.server.idresolution.IdResolutionService
 
getResultsKey() - Method in class org.intermine.webservice.server.idresolution.JobResultsService
 
getResultsKey() - Method in class org.intermine.webservice.server.idresolution.JobStatusService
 
getResultsKey() - Method in class org.intermine.webservice.server.lists.ListShareCreationService
getResultsKey() - Method in class org.intermine.webservice.server.lists.ListShareDetailsService
 
getResultsKey() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationAcceptanceService
 
getResultsKey() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationService
 
getResultsKey() - Method in class org.intermine.webservice.server.query.QueryStoreService
 
getResultsKey() - Method in class org.intermine.webservice.server.query.SavedQueryRetrievalService
 
getResultsKey() - Method in class org.intermine.webservice.server.SchemaListService
 
getResultsKey() - Method in class org.intermine.webservice.server.SessionService
 
getResultsKey() - Method in class org.intermine.webservice.server.SummaryService
 
getResultsKey() - Method in class org.intermine.webservice.server.template.SingleTemplateService
 
getResultsKey() - Method in class org.intermine.webservice.server.user.NewDeletionTokenService
 
getResultsKey() - Method in class org.intermine.webservice.server.user.PermaTokenInfoService
 
getResultsKey() - Method in class org.intermine.webservice.server.user.ReadPreferencesService
 
getResultsKey() - Method in class org.intermine.webservice.server.user.TokenService
 
getResultsKey() - Method in class org.intermine.webservice.server.user.TokensService
 
getResultsKey() - Method in class org.intermine.webservice.server.user.WhoAmIService
 
getResultsKey() - Method in class org.intermine.webservice.server.VersionService
 
getResultsSize(String) - Static method in class org.intermine.dwr.AjaxServices
Return the number of rows of results from the query with the given query id.
getResultsTable(HttpSession, String) - Static method in class org.intermine.web.logic.session.SessionMethods
Given a table identifier, return the cached PagedTable.
getResultsTablesLib() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
getResultsWithoutInit() - Method in class org.intermine.objectstore.query.ClobAccess
Returns the (possibly uninitialised) results object used internally by this object, for use by subclass constructors.
getResultTable() - Method in class org.intermine.model.testmodel.web.widget.AgeGroupLdr
 
getResultTable() - Method in class org.intermine.model.testmodel.web.widget.AgeSalaryLdr
 
getResultTable() - Method in class org.intermine.model.testmodel.web.widget.AgeSeniorityLdr
 
getResultTable() - Method in class org.intermine.model.testmodel.web.widget.CompanyDistLdr
 
getResultTable() - Method in class org.intermine.model.testmodel.web.widget.FullTimeLdr
 
getResultTable() - Method in interface org.intermine.web.logic.widget.DataSetLdr
Return the result table that represents the data from this widget.
getResultTable() - Method in class org.intermine.web.logic.widget.GraphWidgetLoader
 
getReturnToString() - Method in class org.intermine.web.struts.LoginForm
Return the returnToString set by setReturnToURL().
getReverseAliases() - Method in class org.intermine.objectstore.query.Query
Returns the map of String aliases to QuerySelectables and FromElements
getReverseReferenceDescriptor() - Method in class org.intermine.metadata.ReferenceDescriptor
Gets the field in the referenced object that refers back to this class.
getReverseReferenceFieldName() - Method in class org.intermine.metadata.ReferenceDescriptor
Gets the name of the reverse reference field.
getRight() - Method in class org.intermine.objectstore.query.OverlapConstraint
Returns the right OverlapRange.
getRight() - Method in class org.intermine.sql.query.Constraint
Returns the right argument of the constraint.
getRight() - Method in class org.intermine.sql.query.InListConstraint
Returns the right Set of Constants.
getRight() - Method in class org.intermine.sql.writebatch.Row
Returns right.
getRightArgument(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Get the right argument of the given constraint, will return null if passed a ConstraintSet or a MultipleInBagConstraint.
getRightColName() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Returns the right column name.
getRightField() - Method in class org.intermine.api.query.range.ConstraintOptions
Defaults to "end".
getRightOp() - Method in class org.intermine.api.query.range.ConstraintOptions
 
getRootClass() - Method in class org.intermine.pathquery.PathQuery
Returns the root path for this query, if the query verifies correctly.
getRootCVTerms() - Method in class org.intermine.bio.chado.ChadoCV
Return a Set of the root CVTerms in this CV - ie. those with no parents.
getRootElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
getRootElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
 
getRootElement() - Method in class org.intermine.webservice.server.user.UserDataFormatter
 
getRootNode() - Method in class org.intermine.pathquery.LogicExpression
Get the root node.
getRootUrl() - Method in class org.intermine.webservice.client.core.Service
Returns service's root URL.
getRowElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
getRowElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
 
getRowElement() - Method in class org.intermine.webservice.server.user.UserDataFormatter
 
getRowFormatter() - Method in class org.intermine.webservice.server.output.FlatFileFormatter
Get the row formatter
getRowIterator(PathQuery, Page) - Method in class org.intermine.webservice.client.services.QueryService
 
getRowIterator(String, Page) - Method in class org.intermine.webservice.client.services.QueryService
Returns a specific set of the results of a specified PathQuery as an iterator.
getRowIterator(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService
Returns an iterator over a subset of rows for the template when run with the given parameters.
getRowIterator(TemplateQuery, Page) - Method in class org.intermine.webservice.client.services.TemplateService
 
getRowListIterator(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService
Get an iterator over the results of a query.
getRowListIterator(T, Page) - Method in class org.intermine.webservice.client.services.AbstractQueryService
Get an iterator over the results of a query.
getRowListIterator(String, Page) - Method in class org.intermine.webservice.client.services.QueryService
Get an iterator over the results of a query.
getRowListIterator(String) - Method in class org.intermine.webservice.client.services.QueryService
Get an iterator over the results of a query.
getRowListIterator(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService
Get an iterator over the results of a query.
getRowListIterator(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
Get an iterator over the results of a query.
getRowMapIterator(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService
Get an iterator over the results of a query.
getRowMapIterator(T, Page) - Method in class org.intermine.webservice.client.services.AbstractQueryService
Get an iterator over the results of a query.
getRowMapIterator(String, Page) - Method in class org.intermine.webservice.client.services.QueryService
Get an iterator over the results of a query.
getRowMapIterator(String) - Method in class org.intermine.webservice.client.services.QueryService
Get an iterator over the results of a query.
getRowMapIterator(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService
Get an iterator over the results of a query.
getRowMapIterator(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
Get an iterator over the results of a query.
getRows(PathQuery) - Method in class org.intermine.api.mines.LocalMine
 
getRows(String) - Method in class org.intermine.api.mines.LocalMine
 
getRows(PathQuery) - Method in interface org.intermine.api.mines.Mine
Run a path query and get back all the results.
getRows(String) - Method in interface org.intermine.api.mines.Mine
Run a path query and get back all the results.
getRows(PathQuery) - Method in class org.intermine.api.mines.RemoteMine
 
getRows(String) - Method in class org.intermine.api.mines.RemoteMine
 
getRows() - Method in class org.intermine.objectstore.query.ResultsInfo
Returns the estimated number of rows in the results.
getRows() - Method in class org.intermine.sql.query.ExplainResult
Returns the number of rows estimated by the database for this query.
getRows() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return the currently visible rows of the table as a List of Lists of ResultElement objects.
getRows() - Method in class org.intermine.web.tags.table.TableTag
 
getRows(Request, List<String>) - Method in class org.intermine.webservice.client.services.AbstractQueryService
Performs the actual remote request and fetches the results.
getRows(PathQuery, Page) - Method in class org.intermine.webservice.client.services.QueryService
 
getRows(TemplateQuery, Page) - Method in class org.intermine.webservice.client.services.TemplateService
 
getRows() - Method in class org.intermine.webservice.server.core.SubTable
 
getRowsAsLists() - Method in class org.intermine.webservice.client.results.RowResultSet
Get the data for this result set in a parsed form.
getRowsAsLists(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService
Get results for a query as rows of objects.
getRowsAsLists(T, Page) - Method in class org.intermine.webservice.client.services.AbstractQueryService
Get results for a query as rows of objects.
getRowsAsLists(String, Page) - Method in class org.intermine.webservice.client.services.QueryService
Get results for a query as rows of objects.
getRowsAsLists(String) - Method in class org.intermine.webservice.client.services.QueryService
Get results for a query as rows of objects.
getRowsAsLists(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService
Get results for a query as rows of objects.
getRowsAsLists(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
Get results for a query as rows of objects.
getRowsAsMaps() - Method in class org.intermine.webservice.client.results.RowResultSet
Get the data for this result set in a parsed form.
getRowsAsMaps(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService
Get results for a query as rows of objects.
getRowsAsMaps(T, Page) - Method in class org.intermine.webservice.client.services.AbstractQueryService
Get results for a query as rows of objects.
getRowsAsMaps(String, Page) - Method in class org.intermine.webservice.client.services.QueryService
Get results for a query as rows of objects.
getRowsAsMaps(String) - Method in class org.intermine.webservice.client.services.QueryService
Get results for a query as rows of objects.
getRowsAsMaps(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService
Get results for a query as rows of objects.
getRowsAsMaps(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
Get results for a query as rows of objects.
getRowsFromBatch(int, int, int, boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches
Gets a range of rows from within a batch
getRowspan() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
Returns the rowspan.
getRowSpan() - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
Used from JSP in rowspan attr of
getRowsToDelete() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Returns the Set of rows to delete.
getRowsToInsert() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Returns the Set of rows to insert.
getRunner(String, InterMineAPI) - Static method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
getRunningQueryController(String, HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the QueryMonitor object corresponding to a running query id (qid).
getSampleQuery(boolean) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr
 
getSampleSize() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
The sample size, n.
getSampleSize() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
 
getSavedBag(String, String) - Method in class org.intermine.api.bag.SharedBagManager
Perform a query to retrieve a bag's backing SavedBag
getSavedBagId() - Method in class org.intermine.api.profile.StorableBag
 
getSavedBags() - Method in class org.intermine.api.profile.Profile
Get the value of savedBags
getSavedBagsByStatus() - Method in class org.intermine.api.profile.Profile
Get the saved bags in a map of "status key" => map of lists
getSavedBagStatus() - Method in class org.intermine.dwr.AjaxServices
This method gets the latest bags from the session (SessionMethods) and returns them in JSON
getSavedQueries() - Method in class org.intermine.api.profile.Profile
Get the value of savedQueries
getSavedTemplateQuery() - Method in class org.intermine.api.template.ApiTemplate
Gets the saved template query object.
getSavedTemplates() - Method in class org.intermine.api.profile.Profile
Get the users saved templates
getSchema() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Returns the DatabaseSchema used by this ObjectStore.
getSchemaLocation(HttpServletRequest) - Static method in class org.intermine.webservice.server.query.AbstractQueryService
 
getScope() - Method in class org.intermine.web.struts.TemplateForm
Get the template scope.
getScore() - Method in class org.intermine.api.lucene.KeywordSearchHit
score
getScore() - Method in class org.intermine.bio.io.bed.BEDRecord
 
getScore() - Method in class org.intermine.bio.io.gaf.GAFRecord
 
getScore() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the score field of this record.
getScore() - Method in class org.intermine.web.search.KeywordSearchResult
return score
getSearchHits(BrowseHit[], Map<Integer, InterMineObject>) - Static method in class org.intermine.api.lucene.KeywordSearch
 
getSearchIndex(String) - Method in class org.intermine.api.search.SearchRepository
Retrieve a search index for a given type of web searchable objects.
getSearchInfo() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput
 
getSearchItems() - Method in class org.intermine.api.search.SearchRepository
Returns an unmodifiable view of the the search items observed by this repository.
getSearchRepository() - Method in class org.intermine.api.profile.Profile
Get the SearchRepository for this Profile.
getSearchTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices
 
getSearchTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices
 
getSecondFieldName() - Method in class org.intermine.objectstore.query.QueryField
Returns the name of the second field.
getSecondLastClassDescriptor() - Method in class org.intermine.pathquery.Path
Returns the second to last ClassDescriptor in the path.
getSection(Collection<String>) - Method in class org.intermine.pathquery.LogicExpression
Take a Collection of String variable names, and return the part of the Logic Expression that contains those variables.
getSection() - Method in class org.intermine.webservice.server.jbrowse.Segment
 
getSectionTitle() - Method in class org.intermine.web.logic.config.FieldConfig
Get the section title (if sectionOnRight == true).
getSegment() - Method in class org.intermine.webservice.server.jbrowse.Command
 
getSegmentedFeatures() - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return a list of types where one logical feature is represented as multiple rows in the feature table.
getSelect() - Method in class org.intermine.objectstore.query.Query
Gets the SELECT list
getSelect() - Method in interface org.intermine.objectstore.query.Queryable
Returns the SELECT list.
getSelect() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the SELECT list.
getSelect() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Returns the SELECT list.
getSelect() - Method in class org.intermine.sql.query.Query
Gets the list of select fields for this query.
getSelected() - Method in class org.intermine.web.struts.ModifyTemplateForm
Gets the selected templates
getSelected() - Method in class org.intermine.web.struts.WidgetForm
 
getSelectedAsString() - Method in class org.intermine.web.struts.WidgetForm
returns the value of the checkboxes checked by the user on the form.
getSelectedBags() - Method in class org.intermine.web.struts.ModifyBagForm
Gets the selected bags
getSelectedClass() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
getSelectedColumn() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
getSelectedConstraint() - Method in class org.intermine.web.logic.query.DisplayConstraint
Returns the constraint type selected.
getSelectedElements() - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Get a String array of selected bag elements
getSelectedExtraAttribute() - Method in class org.intermine.web.struts.WidgetForm
 
getSelectedExtraValue() - Method in class org.intermine.web.logic.query.DisplayConstraint
If editing an existing LOOKUP constraint return the value selected for the extra constraint field.
getSelectedObjects() - Method in class org.intermine.web.struts.BagUploadConfirmForm
Gets the ids of the selected objects
getSelectedObjects() - Method in class org.intermine.web.struts.SaveBagForm
Gets the selected objects
getSelectedOp() - Method in class org.intermine.web.logic.query.DisplayConstraint
If the bag is selected, return the value setted with the method setSelectedBagOp If editing an existing constraint return the operation used.
getSelectedQueries() - Method in class org.intermine.web.struts.ModifyQueryForm
Gets the selected queries
getSelectedValue() - Method in class org.intermine.web.logic.query.DisplayConstraint
If editing an existing constraint, return the selected value.
getSelectionIds() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
getSelectionInformation() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
The message passed to results page
getSeqClsName() - Method in class org.intermine.bio.dataconversion.GFF3Converter
Return the sequence class name that was passed to the constructor.
getSeqIdentifier(String) - Method in class org.intermine.bio.dataconversion.GFF3SeqHandler
Return the identifier of this sequence, default implementation returns the id passed to it.
getSeqIdentifier(String) - Method in class org.intermine.bio.dataconversion.NcbiGffGFF3SeqHandler
Return the identifier of this sequence, default implementation returns the id passed to it.
getSequence() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Return the sequence Item set by setSequence()
getSequence() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getSequence(Set<Object>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Return the sequence number representing the state of the ObjectStore.
getSequence(Set<Object>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Returns an object representing the current state of the database, for fail-fast concurrency control.
getSequence(Set<Object>) - Method in interface org.intermine.objectstore.ObjectStore
Return the sequence number representing the state of the ObjectStore.
getSequence(Set<Object>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Returns an object representing the current state of the database, for fail-fast concurrency control.
getSequence(Set<Object>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Return the sequence number representing the state of the ObjectStore.
getSequence() - Method in class org.intermine.objectstore.query.Results
Returns the sequence that this Results object was created with
getSequence() - Method in class org.intermine.objectstore.query.ResultsBatches
Returns the sequence that this ResultsBatches object was created with
getSequenceFeatureForSequence(ObjectStore, Sequence) - Static method in class org.intermine.bio.web.export.ResidueFieldExporter
Find the SequenceFeature that references the given Sequence.
getSequenceID() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the sequenceID field of this record.
getSequenceOntology() - Static method in class org.intermine.bio.ontology.SequenceOntologyFactory
 
getSequenceOntology(File, File) - Static method in class org.intermine.bio.ontology.SequenceOntologyFactory
Given an OBO file, create a Sequence Ontology object
getSequenceOntologyRefId() - Method in class org.intermine.bio.dataconversion.BioDBConverter
 
getSequenceOntologyRefId() - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter
 
getSequenceOntologyRefId() - Method in class org.intermine.bio.dataconversion.BioFileConverter
 
getSequencePath() - Method in class org.intermine.bio.web.struts.SequenceExportForm
Gets the selected path
getSerial() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Gets an ID number which is unique in the database.
getSerial() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets an ID number which is unique in the database.
getSerial() - Method in interface org.intermine.objectstore.ObjectStore
Gets an ID number which is unique in the database.
getSerial() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Gets an ID number which is unique in the database.
getSerial() - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Gets an ID number which is unique in the database.
getSerialWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets an ID number which is unique in the database, given a Connection.
getSerialWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Overrides, in order to store recentSequences.
getSeriesLabels() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
getSeriesPath() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
getSeriesValues() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
getService() - Method in class org.intermine.bio.webservice.BEDQueryServlet
 
getService() - Method in class org.intermine.bio.webservice.BioExportServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.bio.webservice.BioExportServlet
 
getService() - Method in class org.intermine.bio.webservice.FastaListServlet
 
getService() - Method in class org.intermine.bio.webservice.FastaQueryServlet
 
getService() - Method in class org.intermine.bio.webservice.GAFQueryServlet
 
getService() - Method in class org.intermine.bio.webservice.GenomicRegionBedServlet
 
getService() - Method in class org.intermine.bio.webservice.GenomicRegionFastaServlet
 
getService() - Method in class org.intermine.bio.webservice.GenomicRegionGFF3Servlet
 
getService() - Method in class org.intermine.bio.webservice.GenomicRegionSearchServlet
 
getService() - Method in class org.intermine.bio.webservice.GFF3ListServlet
 
getService() - Method in class org.intermine.bio.webservice.GFF3QueryServlet
 
getService(String, String) - Method in class org.intermine.webservice.client.core.ServiceFactory
Creates a new service for general use.
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.core.ConfigurableWebServiceServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.core.RestfulServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.core.WebServiceServlet
Implement this to route requests.
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.idresolution.IdResolutionServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.AvailableListsServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.ListRenameServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.ListShareServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.ListSharingInvitationServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.query.QueryUploadServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.search.QuickSearchServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.template.result.TemplateResultServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.template.TemplateToListServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.template.TemplateUploadServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.DeregistrationTokenServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.NewUserServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.PermaTokensServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.WhoAmIServlet
 
getServiceBaseURL() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
getServices() - Method in class org.intermine.webservice.server.ServiceListingHandler
 
getServiceUrl() - Method in interface org.intermine.webservice.client.core.Request
Returns service URL.
getServiceUrl() - Method in class org.intermine.webservice.client.core.RequestImpl
Returns service URL.
getSession() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
Get the session
getSession() - Method in class org.intermine.webservice.server.core.SessionlessRequest
 
getSession(boolean) - Method in class org.intermine.webservice.server.core.SessionlessRequest
 
getSessionIdentifier() - Method in class org.intermine.api.tracker.track.TrackAbstract
Return the session id
getSetter() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the setter Method.
getSetter(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the Method object that is the setter for the field name
getSharedBags(Profile) - Method in class org.intermine.api.bag.BagManager
Fetch the shared bags for the given profile.
getSharedBags(Profile) - Method in class org.intermine.api.bag.SharedBagManager
Return a map containing the bags that the user in input has access because shared by someone else
getSharedBags() - Method in class org.intermine.api.profile.Profile
Return the shared bags for the profile.
getSharedBagsContainingId(Profile, Integer) - Method in class org.intermine.api.bag.BagManager
Fetch bags shared by another user that contain the given id.
getShortName() - Method in class org.intermine.bio.util.OrganismData
Get the short of this organism, eg.
getShowIdentifier() - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
Used from JSP
getShowImmediately() - Method in class org.intermine.web.displayer.ReportDisplayer
 
getShowImmediately() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Should we display this 'splayer immediately, wo/ waiting for the AJAX call?
getShowInHeader() - Method in class org.intermine.web.logic.config.InlineListConfig
 
getShowInInlineCollection() - Method in class org.intermine.web.logic.config.FieldConfig
Return the value of the showInInlineCollection flag
getShowInListAnalysisPreviewTable() - Method in class org.intermine.web.logic.config.FieldConfig
 
getShowInQB() - Method in class org.intermine.web.logic.config.FieldConfig
 
getShowInResults() - Method in class org.intermine.web.logic.config.FieldConfig
Return the value of the showInResults flag
getShowInSummary() - Method in class org.intermine.web.logic.config.FieldConfig
Return the value of the showInSummary flag
getShowLinksToObjects() - Method in class org.intermine.web.logic.config.InlineListConfig
 
getShowLinksToObjects() - Method in class org.intermine.web.logic.results.InlineList
 
getShowOnLeft() - Method in class org.intermine.web.logic.config.Displayer
 
getSimpleClass(Class<? extends FastPathObject>) - Static method in class org.intermine.util.DynamicUtil
Returns the result of decomposeClass if that is a single class, or throws an exception if there are more than one.
getSimpleClass(FastPathObject) - Static method in class org.intermine.util.DynamicUtil
For the given object returns the result of decomposeClass if that is a single class, or throws an exception if there are more than one class.
getSimpleClassName(Class<?>) - Static method in class org.intermine.util.DynamicUtil
Returns the simple class name for the given class or throws an exception if there are more than one.
getSimpleClassName(FastPathObject) - Static method in class org.intermine.util.DynamicUtil
Returns the simple class name for the given object or throws an exception if there are more than one.
getSimpleName() - Method in class org.intermine.metadata.ClassDescriptor
Returns the simple class name described by this ClassDescriptor.
getSimpleObjectClassDescriptors() - Method in class org.intermine.metadata.Model
Return ClassDescriptors for simple objects only - simple objects are light weight objects without an id and with no inheritance.
getSimplePathQuery() - Method in class org.intermine.web.logic.widget.GraphWidget
Returns the pathquery based on the classkey.
getSingleUseKey() - Method in class org.intermine.api.profile.Profile
Return a single use API key for this profile
getSingleUseKey() - Static method in class org.intermine.dwr.AjaxServices
Return the single use API key for the current profile
getSize() - Method in class org.intermine.api.profile.InterMineBag
 
getSize() - Method in class org.intermine.api.profile.InvalidBag
 
getSize() - Method in class org.intermine.api.profile.StorableBag
Returns the size of the bag.
getSize() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Returns the current amount of data, in bytes, held in this object.
getSize() - Method in interface org.intermine.sql.writebatch.Table
Returns the current amount of data, in bytes, held in this object.
getSize() - Method in class org.intermine.sql.writebatch.TableBatch
Returns the current amount of data, in bytes, held in this object.
getSize() - Method in class org.intermine.web.logic.results.DisplayField
Get the size of this collection
getSize() - Method in class org.intermine.web.logic.results.InlineList
 
getSize() - Method in class org.intermine.web.logic.widget.PopulationInfo
 
getSize() - Method in class org.intermine.webservice.client.lists.ItemList
 
getSize() - Method in class org.intermine.webservice.client.results.Page
Get the maximum size of this page.
getSize() - Method in class org.intermine.webservice.server.core.Page
 
getSizeFields() - Method in class org.intermine.web.autocompletion.LuceneObjectClass
getSizeFields
getSizeValues() - Method in class org.intermine.web.autocompletion.LuceneObjectClass
getSizeValues
getSizeValuesForField(String) - Method in class org.intermine.web.autocompletion.LuceneObjectClass
getSizeValuesForField
getSkeleton() - Method in class org.intermine.dataloader.Source
Getter for skeleton.
getSkeletonSource(String, String) - Method in interface org.intermine.dataloader.IntegrationWriter
Converts a string describing the data source into a Source object suitable for passing to the store method as the skeleton source.
getSkeletonSource(String, String) - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Converts a string describing the data source into a Source object suitable for passing to the store method as the skeleton source.
getSome(String...) - Method in class org.intermine.web.security.KeyStorePublicKeySource
 
getSome(String...) - Method in interface org.intermine.web.security.PublicKeySource
Get multiple keys given a set of names.
getSoTerm(DataConverter, Item, String, String) - Static method in class org.intermine.bio.dataconversion.BioStoreHook
Get and store a SO term based on intermine item's class or featureType (if provided).
getSource() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the source field of this record.
getSource(Integer, String) - Method in class org.intermine.dataloader.DataTracker
Retrieve the Source for a specified field of an Object stored in the database.
getSource(String) - Method in class org.intermine.dataloader.ObjectDescription
Gets the source associated with the given fieldname.
getSourceLocations() - Method in class org.intermine.task.project.Project
Get a list of directories to search for sources, specified by 'source.location. properties.
getSourceName() - Method in class org.intermine.bio.web.XRef
 
getSourcePrimaryKeys(Source, Model) - Static method in class org.intermine.dataloader.DataLoaderHelper
Fetch all primary keys for the given source.
getSources() - Method in class org.intermine.task.project.Project
Return a Map from source name to Source
getSpecies() - Method in class org.intermine.bio.util.OrganismData
Get the species of this organism.
getSQLString() - Method in class org.intermine.sql.precompute.PrecomputedTable
Get a "CREATE TABLE" SQL statement for this PrecomputedTable.
getSQLString() - Method in class org.intermine.sql.query.AbstractConstraint
Returns a String representation of this AbstractConstraint object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.AbstractTable
Returns a String representation of this AbstractTable object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.AbstractValue
Returns a String representation of this AbstractValue object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.Constant
Returns a String representation of this Constant object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.Constraint
Returns a String representation of this Constraint object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.ConstraintSet
Returns a String representation of this ConstraintSet object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.Field
Returns a String representation of this Field object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.Function
Returns a String representation of this Function object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.InListConstraint
Returns a String representation of this InListConstraint object, suitable for forming part of an SQL Query.
getSQLString() - Method in class org.intermine.sql.query.NotConstraint
Returns a String representation of this Constraint object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.OrderDescending
Returns a String representation of this AbstractValue object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.Query
Convert this Query into a SQL String query.
getSQLString() - Method in class org.intermine.sql.query.SelectValue
Returns a String representation of this Field object, suitable for forming part of an SQL SELECT list.
getSQLString() - Method in interface org.intermine.sql.query.SQLStringable
Returns a String representation of this object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.SubQuery
Returns a String representation of this SubQuery object, auitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.SubQueryConstraint
Returns a String representation of this SubQueryConstraint object, suitable for forming part of an SQL Query.
getSQLString() - Method in class org.intermine.sql.query.Table
Returns a String representation of this Table object, suitable for forming part of an SQL query.
getSQLStringForPrecomputedTable(String) - Method in class org.intermine.sql.query.Query
Convert this Query into a SQL String query, without regard to the other members of the the UNION, with an extra field in the SELECT list.
getSQLStringNoUnion() - Method in class org.intermine.sql.query.Query
Convert this Query into a SQL String query, without regard to the other members of the UNION.
getSrc() - Method in class org.intermine.web.logic.config.Displayer
Get the source of this displayer
getStainingLevel() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList
 
getStandardDeviation() - Method in class org.intermine.webservice.client.services.QueryService.NumericSummary
 
getStandardIndexStatements(ClassDescriptor, Map<String, IndexStatement>) - Method in class org.intermine.task.CreateIndexesTask
Add indexes for primary keys, indirection tables and 1-N relations to the relevant tables for a given ClassDescriptor
getStar(Model, String) - Static method in class org.intermine.webservice.client.util.PQUtil
Get a list of all the path-strings for the attributes of a given class.
getStart() - Method in interface org.intermine.api.query.range.Range
 
getStart() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the start field of this record.
getStart() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
Get start value
getStart() - Method in class org.intermine.bio.web.model.GenomicRegion
 
getStart() - Method in class org.intermine.objectstore.query.OverlapRange
Returns the left parameter.
getStart() - Method in class org.intermine.objectstore.query.ResultsInfo
Returns the estimated amount of time taken to produce the first row of the results.
getStart() - Method in class org.intermine.sql.query.ExplainResult
Returns the number of page requests before the first row is returned, estimated by the database for this query.
getStart() - Method in class org.intermine.webservice.client.results.Page
Get the start index of this page.
getStart() - Method in class org.intermine.webservice.server.core.Page
Get the index of the first row that is requested.
getStart() - Method in class org.intermine.webservice.server.jbrowse.Segment
 
getStart() - Method in class org.intermine.webservice.server.WebServiceInput
Returns index of first returned result
getStartClass() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getStartClassDescriptor() - Method in class org.intermine.pathquery.Path
Return the ClassDescriptor of the first element in the path.
getStartClassDisplay() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getStartedAt() - Method in interface org.intermine.api.idresolution.Job
 
getStartedAt() - Method in class org.intermine.api.idresolution.ResolutionJob
 
getStartedAt() - Method in class org.intermine.api.idresolution.UpgradeJob
 
getStartingPoints() - Method in class org.intermine.web.logic.aspects.Aspect
Get a List of starting point class names.
getStartRow() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the index of the first row of this page
getState() - Method in class org.intermine.api.profile.InterMineBag
Return the bag state: current, not current, to upgrade
getState() - Method in class org.intermine.api.profile.InvalidBag
 
getState() - Method in class org.intermine.api.profile.StorableBag
Return a string representing the state of this bag (eg.
getState(String) - Method in class org.intermine.web.logic.results.WebState
 
getStatementCreatingTable() - Method in class org.intermine.api.tracker.AbstractTracker
Generate the sql statement to create the table used by the tracker
getStatementCreatingTable() - Method in class org.intermine.api.tracker.KeySearchTracker
 
getStatementCreatingTable() - Method in class org.intermine.api.tracker.ListTracker
Generate the sql statement to create the table used by the tracker
getStatementCreatingTable() - Method in class org.intermine.api.tracker.LoginTracker
Generate the sql statement to create the table used by the tracker
getStatementCreatingTable() - Method in class org.intermine.api.tracker.QueryTracker
Generate the sql statement to create the table used by the tracker
getStatementCreatingTable() - Method in class org.intermine.api.tracker.TemplateTracker
Generate the sql statement to create the table used by the tracker
getStates() - Method in class org.intermine.web.logic.results.WebState
 
getStaticPage(String, String) - Static method in class org.intermine.web.logic.WebUtil
Return the contents of the page given by prefixURLString + '/' + path as a String.
getStatus() - Method in interface org.intermine.api.idresolution.Job
 
getStatus() - Method in class org.intermine.api.idresolution.ResolutionJob
 
getStatus() - Method in class org.intermine.api.idresolution.UpgradeJob
 
getStatus() - Method in class org.intermine.objectstore.query.ResultsInfo
Returns an integer describing the type of estimate getRows() returns.
getStatus() - Method in class org.intermine.webservice.client.lists.ItemList
Any status other than CURRENT indicated this list needs manual attention in the webapp.
getStocksResultSet(Connection) - Method in class org.intermine.bio.dataconversion.StockProcessor
Return the interesting rows from the features table.
getStrain(Set<String>) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
Get strain taxons.
getStrain() - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
 
getStrain(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig
 
getStrain(String) - Method in class org.intermine.bio.util.OrganismRepository
Get strains for given taxon ID
getStrains() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
used for testing
getStrand() - Method in class org.intermine.bio.io.bed.BEDRecord
 
getStrand() - Method in class org.intermine.bio.io.gaf.GAFRecord
 
getStrand() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the strand field of this record.
getStrand() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
Get strand value
getString(String) - Static method in class org.intermine.api.query.codegen.JSStrings
 
getString(String, Object...) - Static method in class org.intermine.api.query.codegen.JSStrings
 
getString() - Method in class org.intermine.metadata.StringUtil.LineWrappedString
Returns the wrapped String.
getString(String) - Method in class org.intermine.webservice.client.results.Item
Get a property known to be a string.
getStringResponse(Request, Integer) - Method in class org.intermine.webservice.client.core.Service
Performs the request and returns the result as a string.
getStringResponse(Request) - Method in class org.intermine.webservice.client.core.Service
Performs the request and returns the result as a string.
getStrings() - Method in class org.intermine.model.StringConstructor
Returns a Collection containing the Strings that form this object, in the correct order.
getStructure() - Method in class org.intermine.web.logic.query.MetadataNode
Returns the structure of the tree.
getStructure() - Method in class org.intermine.web.logic.TreeNode
Returns the structure of the tree.
getStyle() - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
Returns element style.
getStyleClass() - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
Returns css style class of element.
getSubclass() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the subclass if it exists.
getSubclass() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Returns the subclass if it exists.
getSubclass() - Method in class org.intermine.web.logic.querybuilder.SummaryPath
Returns the name of the subclass on this path, if there is one.
getSubClassConstraintPaths() - Method in class org.intermine.pathquery.Path
Returns a Map from simplified path string (with dots instead of colons, and no constraints) to constraint class name.
getSubclasses() - Method in class org.intermine.pathquery.PathQuery
Returns the subclass Map for this query, if the query verifies correctly.
getSubclassValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of subclassValue
getSubDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Return a Set of ClassDescriptors for all classes that directly extend or implement this class or interface.
getSubject() - Method in class org.intermine.web.struts.ContactForm
 
getSubmissionOrganism(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return the row needed for the organism.
getSubmissions(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Return the rows needed for the submission table.
getSubSequence() - Method in class org.intermine.objectstore.query.ClobAccess
Returns true if this object is a subsequence of a main Clob.
getSubtab(String) - Method in class org.intermine.web.logic.results.WebState
 
getSubtabs() - Method in class org.intermine.web.logic.results.WebState
map of tab --> subtab
getSubTitle() - Method in class org.intermine.web.logic.aspects.Aspect
Get the subtitle
getSubTitles() - Method in class org.intermine.web.logic.config.Type
 
getSubtractLists() - Method in class org.intermine.webservice.server.lists.ListInput
 
getSubType() - Method in class org.intermine.webservice.client.core.ContentType
 
getSuffix() - Method in class org.intermine.bio.webservice.AbstractRegionExportService
 
getSuffix() - Method in class org.intermine.bio.webservice.BEDQueryService
 
getSuffix() - Method in class org.intermine.bio.webservice.BioQueryService
 
getSuffix() - Method in class org.intermine.bio.webservice.FastaQueryService
 
getSuffix() - Method in class org.intermine.bio.webservice.GAFQueryService
 
getSuffix() - Method in class org.intermine.bio.webservice.GenomicRegionBedService
 
getSuffix() - Method in class org.intermine.bio.webservice.GenomicRegionFastaService
 
getSuffix() - Method in class org.intermine.bio.webservice.GenomicRegionGFF3Service
 
getSuffix() - Method in class org.intermine.bio.webservice.GFFQueryService
 
getSuffix() - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart
A suffix that may be an HTML tag to appear after this part in the title.
getSummary(Source) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Returns a StringBuffer containing summary information.
getSummary(Source) - Method in class org.intermine.dataloader.HintingFetcher
Returns a StringBuffer containing summary information.
getSummary(PathQuery, String) - Method in class org.intermine.webservice.client.services.QueryService
Get a summary for the values in column of a query.
getSummary(PathQuery, String, Page) - Method in class org.intermine.webservice.client.services.QueryService
Get a summary for the values in column of a query.
getSuperclassDescriptor() - Method in class org.intermine.metadata.ClassDescriptor
Get the super class of this class (may be null).
getSuperclassNames() - Method in class org.intermine.metadata.ClassDescriptor
Return set of superclass class names.
getSuperDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Get a set of ClassDescriptors for the interfaces superclasses that this class implements.
getSuperuser() - Method in class org.intermine.api.profile.Profile
Alias of isSuperUser() for jsp purposes.
getSuperuser() - Method in class org.intermine.api.profile.ProfileManager
Return the super user name set in the properties file
getSuperuserProfile() - Method in class org.intermine.api.profile.ProfileManager
Return the superuser profile set in the properties file
getSuperuserProfile(Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
Return the super user
getSuperUsers() - Method in class org.intermine.api.profile.ProfileManager
Return a list of users with 'superuser' role
getSuperUsers() - Method in class org.intermine.web.struts.ModifySuperUserForm
Get the super users
getSuperUsersProfile() - Method in class org.intermine.api.profile.ProfileManager
Return a list of profile with 'superuser' role
getSwitchable() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return the value on, off, locked depending on the constraint SwitchOffAbility .
getSwitchable() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
Get the switchoffAbility for a constraint.
getSwitchable() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Get the switchable value (on, off, locked).
getSwitchOff(String) - Method in class org.intermine.web.struts.TemplateForm
Get the SwitchOff ability.
getSwitchOffAbility(PathConstraint) - Method in class org.intermine.template.TemplateQuery
Gets the sbitch-off-ability of a constraint.
getSwitchOffAbility() - Method in class org.intermine.template.TemplateValue
Returns the SwitchOffAbility.
getSynonym(Item, String) - Method in class org.intermine.bio.dataconversion.GFF3Converter
Create and add a synonym Item from the given information.
getSynonymResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return the interesting rows from the synonym table.
getSynonyms() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
 
getSynonyms(String, String, String) - Method in class org.intermine.bio.dataconversion.IdResolver
For a particular primary identifier fetch a set of synonyms or return null if id is not a primary identifier for the taxonId given.
getSynonyms(String, String) - Method in class org.intermine.bio.dataconversion.IdResolver
For a particular primary identifier fetch a set of synonyms or return null if id is not a primary identifier for the taxonId given.
getSynonyms() - Method in class org.intermine.bio.dataconversion.UniprotEntry
used to assign sequences
getSynonyms() - Method in class org.intermine.bio.ontology.OboTerm
Get a set of synonyms (Strings) for this term.
getTable() - Method in class org.intermine.sql.query.Field
Returns the table of this field.
getTable() - Method in class org.intermine.web.logic.results.DisplayField
Get the inline results table for this collection
getTable() - Method in class org.intermine.web.struts.TableExportForm
Get the table identifier to look up the PagedTable in the servlet context
getTableCount() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
Returns the number of tables in this query.
getTableDefinition() - Static method in class org.intermine.api.bag.SharingInvite
 
getTableDefinition(Database, ClassDescriptor) - Static method in class org.intermine.sql.DatabaseUtil
 
getTableDisplayer() - Method in class org.intermine.web.logic.config.Type
Get the table Displayer
getTableExportConfigs() - Method in class org.intermine.web.logic.config.WebConfig
Return a Map of TableExportConfig.id to TableExportConfig objects.
getTableFieldConfigs() - Method in class org.intermine.web.logic.results.InlineResultsTable
 
getTableFields(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns a Fields object of FieldDescriptors in the given table-mastering ClassDescriptor.
getTableid() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
getTableInfo(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Produces metadata for a given table, caching it to save time.
getTableMaster(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns the name of the table in which to store a row for the given ClassDescriptor.
getTableName() - Method in class org.intermine.api.tracker.track.KeySearchTrack
 
getTableName() - Method in class org.intermine.api.tracker.track.ListTrack
Return the table name where the track has to be saved
getTableName() - Method in class org.intermine.api.tracker.track.LoginTrack
Return the table name where the track has to be saved
getTableName() - Method in class org.intermine.api.tracker.track.QueryTrack
 
getTableName() - Method in class org.intermine.api.tracker.track.TemplateTrack
Return the table name where the track has to be saved
getTableName() - Method in interface org.intermine.api.tracker.track.Track
Return the table name where the track has to be saved
getTableName(ClassDescriptor) - Static method in class org.intermine.sql.DatabaseUtil
Creates a table name for a class descriptor
getTableSize(String, Connection) - Method in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
Returns the approximate number of rows in a table.
getTableSize(String, Connection) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Returns the approximate number of rows in a table.
getTabLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Returns link which gives results as lines, where values are tab separated.
getTag() - Method in class org.intermine.bio.web.model.GenomicRegion
 
getTagById(int) - Method in class org.intermine.api.profile.TagManager
Get Tag by object id.
getTagManager() - Method in interface org.intermine.api.API
 
getTagManager() - Method in class org.intermine.api.InterMineAPI
 
getTagManager() - Method in class org.intermine.api.profile.ProfileManager
Return the TagManager for adding, removing and fetching Tags assigned to templates, bags and classes.
getTagManager() - Method in class org.intermine.api.profile.TagManagerFactory
 
getTagName() - Method in class org.intermine.api.search.TaggingEvent
 
getTags(String, String, String, String) - Method in class org.intermine.api.profile.TagManager
Deprecated.
There are typed methods that are more suitable. Use them instead.
getTags(ApiTemplate, Profile) - Method in class org.intermine.api.template.TemplateManager
For a (public or private) template, return all the tags.
getTags(String) - Static method in class org.intermine.dwr.AjaxServices
Returns all tags of specified tag type together with prefixes of these tags.
getTags() - Method in class org.intermine.webservice.client.lists.ItemList
Modifying the returned set will not change the underlying tags collection.
getTags(ItemList) - Method in class org.intermine.webservice.client.services.ListService
Get the most current tag set for a list.
getTags() - Method in class org.intermine.webservice.server.lists.ListInput
 
getTagsByName(String, Profile, String) - Method in class org.intermine.api.profile.TagManager
Return all the tags with the given tag name, optionally filtered by tag-type.
getTagsByType(String) - Method in class org.intermine.api.profile.TagManager
Return all tags of given type.
getTagsForBag(InterMineBag, Profile) - Method in class org.intermine.api.bag.BagManager
Get a list of tags for a given bag.
getTagString() - Method in class org.intermine.webservice.client.services.ListService.ListOperationInfo
Get the tags joined in the manner required for the list service.
getTagType() - Method in class org.intermine.api.profile.StorableBag
 
getTagType() - Method in interface org.intermine.api.profile.Taggable
Poly-Morphic Constant.
getTagType() - Method in class org.intermine.api.template.ApiTemplate
 
getTagValues() - Method in class org.intermine.bio.ontology.OboTerm
Gets the tagValues.
getTarget() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the first value of the Target field from the attributes of this record.
getTargetModel() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Return the Model that was passed to the constructor.
getTargets() - Method in class org.intermine.webservice.client.widget.Widget
 
getTargetType() - Method in class org.intermine.api.bag.AdditionalConverter
 
getTaxonId() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
 
getTaxonId(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
 
getTaxonId() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getTaxonId() - Method in class org.intermine.bio.util.OrganismData
Get the taxonId of this organism.
getTaxonIds(Set<String>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
 
getTaxonIds(PathQuery, HttpSession) - Static method in class org.intermine.bio.web.logic.SequenceFeatureExportUtil
Get organism taxon ids info from PathQuery
getTaxonIds(PathQuery, InterMineAPI, Profile) - Static method in class org.intermine.bio.web.logic.SequenceFeatureExportUtil
 
getTaxonInfo(InterMineAPI, int) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner
Query the information of all organisms and their taxon ids.
getTaxons() - Method in class org.intermine.bio.dataconversion.IdResolver
Return a set of taxon id.
getTaxonsAndClassNames() - Method in class org.intermine.bio.dataconversion.IdResolver
Get a set of keys (taxon id + class name) resolver holds
getTemplate(String) - Method in class org.intermine.api.profile.Profile
get a template
getTemplate(Profile, String, String) - Method in class org.intermine.api.template.TemplateManager
Fetch a template with the scope provided, possible values are defined in Scope class.
getTemplate(String) - Method in class org.intermine.webservice.client.services.TemplateService
Get the template with the given name, if accessible.
getTemplateButton() - Method in class org.intermine.web.struts.ModifyTemplateForm
 
getTemplateLabel() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Get the template label.
getTemplateManager() - Method in interface org.intermine.api.API
 
getTemplateManager() - Method in class org.intermine.api.InterMineAPI
 
getTemplateManager() - Static method in class org.intermine.api.query.PathQueryAPI
Returns the TemplateManager for access to global and user template queries.
getTemplateName() - Method in class org.intermine.api.tracker.track.TemplateTrack
Return the template name
getTemplateNames() - Method in class org.intermine.webservice.client.services.TemplateService
Get the names of the templates to which the current user has access.
getTemplates() - Method in class org.intermine.web.search.KeywordSearchResult
templates associated with this class
getTemplates() - Method in class org.intermine.webservice.client.services.TemplateService
Get the templates to which the current user has access.
getTemplateService() - Method in class org.intermine.webservice.client.core.ServiceFactory
Return a new QueryService for getting query results from.
getTemplatesForType(String) - Method in class org.intermine.webservice.client.services.TemplateService
Get all the templates with constraints which constrain paths of a certain type.
getTemplateSummariser() - Method in interface org.intermine.api.API
 
getTemplateSummariser() - Method in class org.intermine.api.InterMineAPI
 
getTemplateTracker() - Method in class org.intermine.api.tracker.TrackerDelegate
Return the tracker template
getTemplateTracksPercentage(String) - Method in class org.intermine.dwr.TrackAjaxServices
 
getTemplateTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices
 
getTemporaryListName() - Method in class org.intermine.webservice.server.lists.ListInput
 
getTermIdNameMap(Reader) - Method in class org.intermine.bio.ontology.OboParser
Parse an OBO file to produce a map from ontology term id to name.
getTestCount() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
The test count represents the number of tests that will be performed.
getTestCount() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
 
getText() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionType
 
getText() - Method in class org.intermine.web.logic.config.HeaderConfigLink
 
getText() - Method in class org.intermine.web.logic.TreeNode
Get the text that was passed to the constructor
getText() - Method in class org.intermine.web.struts.BuildBagForm
Get the text string
getTextToFind() - Method in class org.intermine.web.struts.FindInListForm
 
getTgtLocation() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Return the tgtLocation Item set by setTgtLocation()
getTgtModel() - Method in class org.intermine.bio.dataconversion.GFF3Converter
Return the
getTgtOrganism() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Return the tgtOrganism Item set by setTgtOrganism()
getTgtSequence() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Get the target Sequence Item set by setTgtSequence().
getThickEnd() - Method in class org.intermine.bio.io.bed.BEDRecord
 
getThickEnd() - Method in class org.intermine.bio.io.gaf.GAFRecord
 
getThickStart() - Method in class org.intermine.bio.io.bed.BEDRecord
 
getThickStart() - Method in class org.intermine.bio.io.gaf.GAFRecord
 
getThreePrimeUTR() - Method in class org.intermine.bio.web.model.GeneModel
Get the threePrimeUTR if present.
getTickleCount() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Find out how many times tickle has been called.
getTileName() - Method in class org.intermine.web.logic.aspects.Aspect
Get the name of tile/page to embed in the centre of the data set homepage
getTime() - Method in class org.intermine.sql.query.DummyExplainResult
Returns an estimate of the time it will take to complete the query.
getTime() - Method in class org.intermine.sql.query.ExplainResult
Returns an estimate of the time it will take to complete the query.
getTimeLimit() - Method in class org.intermine.sql.precompute.QueryOptimiserContext
Returns the time limit.
getTimestamp() - Method in class org.intermine.api.tracker.track.TrackAbstract
Return the timestamp of the event
getTitle() - Method in class org.intermine.api.bag.AdditionalConverter
 
getTitle() - Method in class org.intermine.api.profile.InterMineBag
The user-friendly title for this object.
getTitle() - Method in class org.intermine.api.profile.InvalidBag
 
getTitle() - Method in interface org.intermine.api.search.WebSearchable
The user-friendly title for this object.
getTitle() - Method in class org.intermine.pathquery.PathQuery
Gets the title for this query.
getTitle() - Method in class org.intermine.template.TemplateQuery
 
getTitle() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return the last class in the path and fieldname as the title for the constraint.
getTitle() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getTitle() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
Get the title
getTitle() - Method in class org.intermine.web.logic.widget.Widget
Get the widget title
getTitle() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
title of the widget
getTitle() - Method in class org.intermine.web.struts.TemplateSettingsForm
Return the title
getTitle() - Method in class org.intermine.webservice.client.widget.Widget
 
getTitleMain() - Method in class org.intermine.web.logic.results.ReportObject
Used by JSP
getTitles() - Method in class org.intermine.web.logic.config.HeaderConfigTitle
 
getTitleSub() - Method in class org.intermine.web.logic.results.ReportObject
Used by JSP
getToggledElements() - Static method in class org.intermine.dwr.AjaxServices
This method gets a map of ids of elements that were in the past (during session) toggled and returns them in JSON
getToggledElements() - Method in class org.intermine.web.logic.results.WebState
Gets map of ids of elements that were in the past (during session) toggled - if they are opened or closed.
getToken() - Method in class org.intermine.api.bag.SharingInvite
 
getToken() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
getToken() - Method in class org.intermine.web.struts.PasswordResetForm
Gets the value of token.
getToken() - Method in class org.intermine.webservice.server.user.DeletionTokenInfoService
 
getTokenUrl() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
 
getTokenUrl() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
 
getTokenUrl() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
 
getTopDownLevelTraversal() - Method in class org.intermine.metadata.Model
Return the classes in the model in level order from shallowest to deepest, the order of nodes at any given level is undefined.
getTotalHits() - Method in class org.intermine.api.lucene.ResultsWithFacets
 
getTrackDescription() - Method in class org.intermine.bio.web.struts.BEDExportForm
 
getTracker(String, Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.factory.TrackerFactory
Return the tracker instantiated with the reflection
getTracker(String) - Method in class org.intermine.api.tracker.TrackerDelegate
Return the tracker specified in input
getTrackerDelegate() - Method in interface org.intermine.api.API
 
getTrackerDelegate() - Method in class org.intermine.api.InterMineAPI
 
getTrackers() - Method in class org.intermine.api.tracker.TrackerDelegate
Return the trackers saved in the TrackerManager
getTrackTableName() - Method in class org.intermine.api.tracker.AbstractTracker
Return the table's name associated to the tracker
getTrail() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
Get the trail URL parameter for this trail element.
getTranscript() - Method in class org.intermine.bio.web.model.GeneModel
Get the transcript this gene model represents
getTransitiveOver() - Method in class org.intermine.bio.ontology.OboTypeDefinition
 
getTranslator() - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Returns the Translator associated with the underlying ObjectStoreTranslatingImpl.
getTranslator() - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Return the Translator that was passed to the constructor.
getType() - Method in class org.intermine.api.bag.BagQueryUpgrade
 
getType() - Method in class org.intermine.api.beans.ObjectDetails
 
getType() - Method in interface org.intermine.api.idresolution.Job
 
getType() - Method in interface org.intermine.api.idresolution.JobInput
 
getType() - Method in class org.intermine.api.idresolution.ResolutionJob
 
getType() - Method in class org.intermine.api.idresolution.UpgradeJob
 
getType() - Method in class org.intermine.api.lucene.KeywordSearchFacetData
type of facet
getType() - Method in class org.intermine.api.profile.InterMineBag
Get the type of this bag (a class from InterMine model)
getType() - Method in class org.intermine.api.profile.InvalidBag
 
getType() - Method in class org.intermine.api.profile.StorableBag
Get the unqualified name of class that the objects in this bag represent.
getType() - Method in class org.intermine.api.results.Column
Return the type of this Column
getType() - Method in interface org.intermine.api.results.ResultCell
 
getType() - Method in class org.intermine.api.results.ResultElement
Get the type
getType() - Method in class org.intermine.api.tracker.track.ListTrack
Return the class type of items contained into the list
getType() - Method in class org.intermine.bio.dataconversion.UniprotEntry.Dbref
 
getType() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return the type field of this record.
getType() - Method in class org.intermine.bio.ontology.OboTermSynonym
Get the synonym type.
getType() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions
 
getType(FieldDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Return the java type of a particular field.
getType() - Method in class org.intermine.dataloader.Source
 
getType() - Method in class org.intermine.metadata.AttributeDescriptor
Get the type of the attribute - either name of primitive or fully qualified class name.
getType() - Method in class org.intermine.metadata.ClassDescriptor
Returns the Class described by this ClassDescriptor.
getType() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the type of the field.
getType() - Method in class org.intermine.objectstore.query.Clob
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.ObjectStoreBag
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.OrderDescending
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.PathExpressionField
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryCast
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryClass
Gets the Java class represented by this QueryClass
getType() - Method in class org.intermine.objectstore.query.QueryClassBag
Gets the Java class represented by this QueryClassBag.
getType() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryCollectionReference
Gets the Java class of this QueryReference.
getType() - Method in class org.intermine.objectstore.query.QueryExpression
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryField
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryForeignKey
Gets the Java class of this QueryReference.
getType() - Method in class org.intermine.objectstore.query.QueryFunction
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryObjectReference
Gets the Java class of this QueryReference.
getType() - Method in interface org.intermine.objectstore.query.QueryOrderable
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryReference
Gets the Java class of this QueryReference.
getType() - Method in interface org.intermine.objectstore.query.QuerySelectable
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryValue
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.WidthBucketFunction
Get Java type represented by this item.
getType() - Method in class org.intermine.pathquery.Node
Gets the value of type
getType(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint
A static method to get the type of this constraint if it is a sub-class constraint, or otherwise return null.
getType() - Method in class org.intermine.pathquery.PathConstraintSubclass
Returns the class that the constraint is constraining to.
getType() - Method in class org.intermine.task.project.Project
Return the type of this project
getType() - Method in class org.intermine.task.project.Source
Get the type of this object.
getType() - Method in class org.intermine.web.logic.bag.WebJobInput
 
getType() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns the type of the value represented by this path, as a string.
getType() - Method in class org.intermine.web.logic.results.ReportObject
Get the unqualified class name for the report object.
getType() - Method in class org.intermine.web.logic.WebUtil.HeadResource
 
getType() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
 
getType() - Method in class org.intermine.web.search.KeywordSearchResult
returns the name of the class for this object (category)
getType() - Method in class org.intermine.web.struts.BuildBagForm
Get the bag type
getType() - Method in class org.intermine.web.struts.CSVExportForm
Return the export type: "tab", etc.
getType() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
Return whether or not this trail element refers to a table.
getType() - Method in class org.intermine.web.struts.TableExportForm
Return the export type: "tab", etc.
getType() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Returns type of tag.
getType() - Method in class org.intermine.webservice.client.core.ContentType
 
getType() - Method in interface org.intermine.webservice.client.core.Request
 
getType() - Method in class org.intermine.webservice.client.core.RequestImpl
getType() - Method in class org.intermine.webservice.client.lists.ItemList
 
getType() - Method in class org.intermine.webservice.client.results.Item
Get the type of this object.
getType() - Method in class org.intermine.webservice.server.core.TableCell
 
getType(String) - Method in class org.intermine.webservice.server.jbrowse.Command
 
getType() - Method in class org.intermine.webservice.server.lists.ListInput
 
getType() - Method in class org.intermine.webservice.server.lists.ListsServiceInput
 
getTypeByName(String) - Static method in class org.intermine.metadata.TypeUtil
Returns the Class for a given name (promoting primitives to their container class) and returning null if the name does not refer to any known class.
getTypeClass() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getTypeClsString() - Method in class org.intermine.api.results.Column
Get the column type unqualified as a String
getTypeForColumn(int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return the class from the data model for the data displayed in indexed column.
getTypes() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the comma separated unqualified class names for which this displayer should be displayed.
getTypes() - Method in class org.intermine.web.logic.config.WebConfig
Get a map from fully qualified class name to the Type config for that class
getUcscCompatibleCheck() - Method in class org.intermine.bio.web.struts.BEDExportForm
 
getUid() - Method in interface org.intermine.api.idresolution.Job
 
getUid() - Method in class org.intermine.api.idresolution.ResolutionJob
 
getUid() - Method in class org.intermine.api.idresolution.UpgradeJob
 
getUnencodedUrl() - Method in interface org.intermine.webservice.client.core.Request
 
getUnencodedUrl() - Method in class org.intermine.webservice.client.core.RequestImpl
 
getUnformatted() - Method in class org.intermine.web.logic.results.ReportObject.TitleValue
Get the unformatted version that is just the field value.
getUnion() - Method in class org.intermine.sql.query.Query
Returns the List of queries in the UNION set of this query.
getUniprot() - Method in class org.intermine.bio.util.OrganismData
 
getUniprotAccession() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
getUniqueIdentifier() - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
eg. primaryIdentifier
getUniqueIdentifier(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig
 
getUniqueInteger(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Return a unique integer from a SEQUENCE in the database.
getUniqueItemId(String) - Method in class org.intermine.dataconversion.DataConverter
List of unique identifiers and their refIds.
getUnmatchedIdentifiers() - Method in class org.intermine.webservice.client.lists.ItemList
Get the identifiers used in creating or appending to this list that could not be resolved to any objects.
getUnqualifiedClassName() - Method in class org.intermine.web.logic.config.Type
 
getUnqualifiedName() - Method in class org.intermine.metadata.ClassDescriptor
Returns unqualified name of class described by this ClassDescriptor.
getUnresolved() - Method in class org.intermine.api.bag.BagQueryResult
Deprecated.
Use getUnresolvedIdentifiers
getUnresolvedIdentifiers() - Method in class org.intermine.api.bag.BagQueryResult
Get all the unresolved identifiers.
getUnusedListName() - Method in class org.intermine.webservice.client.services.ListService.ListOperationInfo
Get a name for the list if none has been supplied.
getUpdatedPathQuery() - Method in class org.intermine.api.profile.PathQueryUpdate
Return a new pathquery updated to the new model
getUrl() - Method in class org.intermine.api.mines.LocalMine
 
getUrl() - Method in interface org.intermine.api.mines.Mine
 
getUrl() - Method in class org.intermine.api.mines.RemoteMine
 
getUrl() - Method in class org.intermine.bio.web.XRef
 
getURL() - Method in class org.intermine.sql.Database
Gets the URL from this database
getUrl() - Method in class org.intermine.web.logic.aspects.AspectSource
Get the URL back to source website.
getUrl() - Method in class org.intermine.web.logic.config.HeaderConfigLink
 
getUrl() - Method in class org.intermine.web.logic.WebUtil.HeadResource
 
getUrl() - Method in class org.intermine.webservice.client.core.Service
Returns service URL Example: http://www.flymine.org/query/service/query/results
getUrlField() - Method in class org.intermine.api.bag.AdditionalConverter
 
getUseBagConstraint(String) - Method in class org.intermine.web.struts.TemplateForm
Get the value of useBagConstraint for given constraint key.
getUseJoin() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
getUser() - Method in class org.intermine.sql.Database
Gets the username for this Database
getUserAndGlobalTemplates(Profile) - Method in class org.intermine.api.template.TemplateManager
Fetch all user and global templates in a single map for the given user.
getUserBag(Profile, String) - Method in class org.intermine.api.bag.BagManager
Fetch a user bag by name.
getUserBags(Profile) - Method in class org.intermine.api.bag.BagManager
Fetch bags for the given profile.
getUserBagsContainingId(Profile, Integer) - Method in class org.intermine.api.bag.BagManager
Fetch user bags that contain the given id.
getUserBagsWithTag(Profile, String) - Method in class org.intermine.api.bag.BagManager
Fetch bags from given protocol with a particular tag assigned to them.
getUserBagsWithTags(Profile, List<String>) - Method in class org.intermine.api.bag.BagManager
Give me profile bags matching a set of tags
getUserId() - Method in class org.intermine.api.profile.Profile
Get the value of userId
getUserLogin(Connection) - Method in class org.intermine.api.tracker.LoginTracker
Return the number of access for each user
getUserLogin() - Method in class org.intermine.api.tracker.TrackerDelegate
Return the number of access for each user
getUsername() - Method in class org.intermine.api.profile.Profile
Get the value of username
getUserName() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
The name of the user logged in when this info was generated
getUserName() - Method in class org.intermine.api.tracker.track.TrackAbstract
Return the user name
getUsername() - Method in class org.intermine.api.util.AnonProfile
 
getUsername() - Method in class org.intermine.web.struts.CreateAccountForm
 
getUsername() - Method in class org.intermine.web.struts.LoginForm
Gets the value of username The user name is always returned in LOWER CASE.
getUsername() - Method in class org.intermine.web.struts.RequestPasswordForm
Gets the value of username
getUserName() - Method in class org.intermine.webservice.server.WebServiceInput
 
getUsernameForToken(String) - Method in class org.intermine.api.profile.ProfileManager
Returns the username associated with the given token, if the token is valid.
getUserOrGlobalTemplate(Profile, String) - Method in class org.intermine.api.template.TemplateManager
Fetch a user or global template by name.
getUserProfile() - Method in class org.intermine.api.InterMineAPI
 
getUserProfile(String) - Method in class org.intermine.api.profile.ProfileManager
Perform a query to retrieve a user's backing UserProfile
getUserProfile(Integer) - Method in class org.intermine.api.profile.ProfileManager
Perform a query to retrieve a user's backing UserProfile
getUserProfileWriter() - Method in class org.intermine.api.profile.InterMineBag
 
getUserProfileWriter() - Method in class org.intermine.api.profile.InvalidBag
 
getUserProfileWriter() - Method in class org.intermine.api.profile.StorableBag
Get a reference to a connection to the database where user data is persisted.
getUserProperties() - Method in class org.intermine.task.project.Action
Return a list of UserProperty objects.
getUsersSharingBag(String, String) - Method in class org.intermine.api.bag.BagManager
Return the users sharing the list given in input, not the owner
getUsersSharingBag(String) - Method in class org.intermine.dwr.AjaxServices
Return the list of users who have access to this bag because it has been shared with them.
getUsersWithAccessToBag(StorableBag) - Method in class org.intermine.api.bag.SharedBagManager
Return the users this bag is shared with.
getUserTagNames(String, Profile) - Method in class org.intermine.api.profile.TagManager
Returns names of tags of specified user and tag type.
getUserTagNames(String, String) - Method in class org.intermine.api.profile.TagManager
Deprecated.
It is better to use the typed methods instead.
getUserTags(String) - Method in class org.intermine.api.profile.TagManager
Returns tags of specified user.
getUserTags(Profile) - Method in class org.intermine.api.profile.TagManager
Returns tags of specified user.
getUserTemplate(Profile, String) - Method in class org.intermine.api.template.TemplateManager
Fetch a user template by name.
getUserToken() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
A token for the user.
getUserWithUniqueMapping(String, String) - Method in class org.intermine.api.profile.PreferencesManager
 
getUUID() - Method in class org.intermine.webservice.server.user.DeletionToken
 
getValidGlobalTemplates() - Method in class org.intermine.api.template.TemplateManager
Return a map from template name to template query containing superuser templates that are tagged as public and are valid for the current data model.
getValidOps() - Method in class org.intermine.web.logic.query.DisplayConstraint
Given the path being constrained return the valid constraint operations.
getValidRangeTargets() - Static method in class org.intermine.api.query.MainHelper
 
getValue() - Method in class org.intermine.api.lucene.KeywordSearchFacet
selected value
getValue() - Method in class org.intermine.api.profile.BagValue
 
getValue() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
Returns the value of the entry.
getValue() - Method in class org.intermine.api.results.flatouterjoins.MultiRowLaterValue
Returns the value of the entry.
getValue() - Method in class org.intermine.api.results.flatouterjoins.MultiRowValue
Returns the value of the entry.
getValue() - Method in class org.intermine.bio.dataconversion.UniprotConfig.IdentifierConfig
 
getValue() - Method in class org.intermine.bio.dataconversion.UniprotEntry.Dbref
 
getValue() - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject
Returns the value.
getValue() - Method in class org.intermine.objectstore.query.QueryCast
Returns the QueryEvaluable that is the actual value.
getValue() - Method in class org.intermine.objectstore.query.QueryValue
Returns the object that is the actual value.
getValue() - Method in class org.intermine.objectstore.query.UnknownTypeValue
Returns the value.
getValue(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint
A static method for accessing values without having to handle the subclasses manually.
getValue() - Method in class org.intermine.pathquery.PathConstraintAttribute
Returns the value that the constraint is constraining to.
getValue() - Method in class org.intermine.pathquery.PathConstraintLookup
Returns the lookup value for this constraint.
getValue() - Method in class org.intermine.sql.query.OrderDescending
Returns the value.
getValue() - Method in class org.intermine.sql.query.SelectValue
Gets the AbstractValue from this object.
getValue() - Method in class org.intermine.task.project.UserProperty
Set the property value
getValue() - Method in class org.intermine.template.TemplateValue
Returns value.
getValue() - Method in class org.intermine.web.logic.config.InlineListObject
Fetch the column value, ie "Zerknullt" for Synonyms of a Gene
getValue() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
Get a string representation of the constraint value to be displayed.
getValue() - Method in class org.intermine.web.logic.results.ReportObjectField
Get field value
getValue() - Method in class org.intermine.web.logic.template.ConstraintInput
Returns constraint value.
getValue() - Method in class org.intermine.webservice.client.template.TemplateParameter
Returns value.
getValue() - Method in class org.intermine.webservice.server.core.Pair
 
getValue() - Method in class org.intermine.xml.full.Attribute
Get the value of this field
getValueHasDisplayer() - Method in class org.intermine.web.logic.results.ReportObjectField
Does the field have a custom displayer defined for the value?
getValueMap() - Method in class org.intermine.sql.precompute.PrecomputedTable
Gets a Map from AbstractValue to SelectValue for the Query in this PrecomputedTable.
getValues() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ExpressionList
Get the internal list of expressions
getValues() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ExpressionList
Get the internal list of expressions
getValues() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList
Get the internal map of expressions
getValues(String) - Method in class org.intermine.dataloader.EquivalentObjectHints
Returns a Set of values that were in the database for a particular class and fieldname.
getValues() - Static method in class org.intermine.metadata.ConstraintOp
Get the the internal list of ConstraintOps (Only for use in webapp)
getValues(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint
Get the values for a constraint.
getValues() - Method in class org.intermine.pathquery.PathConstraintMultiValue
Returns the value collection that the constraint is constraining to.
getValues() - Method in class org.intermine.template.TemplateValue
 
getValues() - Method in class org.intermine.webservice.client.template.TemplateParameter
 
getValuesForField(String) - Method in class org.intermine.web.autocompletion.LuceneObjectClass
getValuesForField
getValuesForField(String, int) - Method in class org.intermine.web.autocompletion.LuceneObjectClass
getValuesForField
getValuesFromInput(TemplateQuery, TemplateResultInput) - Static method in class org.intermine.web.logic.template.Templates
Creates a map from input to be used later to populate the template.
getVariableNames() - Method in class org.intermine.pathquery.LogicExpression
Get the Set of variable names.
getVerboseQueryLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets the verboseQueryLog configuration option.
getVerboseQueryLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Gets the verboseQueryLog configuration option.
getVersion() - Method in class org.intermine.api.profile.ProfileManager
Returns the version number of the data format in the database for this ProfileManager.
getVersion() - Method in class org.intermine.metadata.Model
 
getVersion() - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns the database format version.
getVersion() - Method in class org.intermine.sql.Database
Get the version number of the database as a string.
getVersion() - Method in class org.intermine.webservice.client.core.Service
 
getView() - Method in class org.intermine.pathquery.PathQuery
Returns the current view list.
getView() - Method in class org.intermine.web.struts.TemplateForm
Get the selected alternative view name.
getViewPaths() - Method in class org.intermine.api.results.ExportResultsIterator
 
getViews() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getVisibleColumnCount() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return the number of visible columns.
getVisibleIndexes() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Returns indexes of columns, that should be displayed.
getWarnings() - Method in class org.intermine.webservice.server.query.result.XMLValidator
Returns warnings occurred during parsing xml.
getWarnings() - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler
Returns warning occurred during parsing xml.
getWebConfig() - Static method in class org.intermine.web.context.InterMineContext
 
getWebConfig(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods
 
getWebConfig(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
 
getWebConfig() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
getWebProperties() - Static method in class org.intermine.web.context.InterMineContext
 
getWebProperties(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Returns the web properties.
getWebProperties(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods
Returns the web properties.
getWebProperties(HttpServletRequest) - Static method in class org.intermine.web.struts.InterMineAction
Get the web proprties.
getWebResultsExecutor(Profile) - Method in interface org.intermine.api.API
 
getWebResultsExecutor(Profile) - Method in class org.intermine.api.InterMineAPI
 
getWebSearchableMap(String) - Method in class org.intermine.api.search.GlobalRepository
Get a map from name -> object for all the websearchables of the given type.
getWebSearchableMap(String) - Method in class org.intermine.api.search.SearchRepository
Get a map from name -> object for all the websearchables of the given type.
getWebSearchablesByType(String) - Method in class org.intermine.api.profile.Profile
Return a WebSearchable Map for the given type.
getWebState(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Get WebState object that is used for saving state of webapp GUI.
getWebTable() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
getWhere() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getWhere() - Method in class org.intermine.sql.query.Query
Gets the Set of constraints in the where clause of this query.
getWhereBuffer() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getWhichInput() - Method in class org.intermine.web.struts.BuildBagForm
Get the method the user used to upload the bag.
getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions) - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig
 
getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getWidget(String) - Method in class org.intermine.webservice.client.services.WidgetService
 
getWidgetid() - Method in class org.intermine.web.struts.WidgetForm
 
getWidgetId() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
Get the name or id of the widget
getWidgets() - Method in class org.intermine.web.logic.config.Type
 
getWidgets() - Method in class org.intermine.web.logic.config.WebConfig
 
getWidgets() - Method in class org.intermine.webservice.client.services.WidgetService
 
getWidgetService() - Method in class org.intermine.webservice.client.core.ServiceFactory
Return the WidgetService for retrieving widget information.
getWidgetTitle() - Method in class org.intermine.web.struts.WidgetForm
used on results page for description: "results for widget XYZ"
getWidgetTotal() - Method in class org.intermine.model.testmodel.web.widget.AgeGroupLdr
 
getWidgetTotal() - Method in class org.intermine.model.testmodel.web.widget.AgeSalaryLdr
 
getWidgetTotal() - Method in class org.intermine.model.testmodel.web.widget.AgeSeniorityLdr
 
getWidgetTotal() - Method in class org.intermine.model.testmodel.web.widget.CompanyDistLdr
 
getWidgetTotal() - Method in class org.intermine.model.testmodel.web.widget.FullTimeLdr
 
getWidgetTotal() - Method in interface org.intermine.web.logic.widget.DataSetLdr
This method is used to calculate the 'not analysed' total displayed on each widget
getWidgetTotal() - Method in class org.intermine.web.logic.widget.GraphWidgetLoader
 
getWidgetTotal() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
 
getWidgetType() - Method in class org.intermine.webservice.client.widget.Widget
 
getWidgetType(WidgetConfig) - Method in class org.intermine.webservice.server.widget.WidgetProcessorImpl
 
getWidth() - Method in class org.intermine.sql.query.ExplainResult
Returns the width of the data returned by the database for this query.
getWidth() - Method in class org.intermine.webservice.server.jbrowse.Segment
 
getWildCards() - Method in interface org.intermine.api.idresolution.JobInput
 
getWildCards() - Method in class org.intermine.web.logic.bag.WebJobInput
 
getWithinOptions() - Method in class org.intermine.api.query.range.AbstractHelper
 
getWithinOptions() - Method in class org.intermine.model.testmodel.query.range.EmploymentPeriodHelper
 
getWorkingTemplates(Profile) - Method in class org.intermine.api.template.TemplateManager
Fetch all user and global templates that are valid.
getWorkingTemplates() - Method in class org.intermine.api.template.TemplateManager
Fetch all global templates that are valid.
getWormIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a worm id resolver
getWormIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a worm id resolver
getWormIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
Create a worm id resolver
getWriter() - Method in class org.intermine.webservice.server.output.StreamedOutput
Returns associated writer
getWrittenResultsCount() - Method in class org.intermine.bio.web.export.BEDExporter
 
getWrittenResultsCount() - Method in class org.intermine.bio.web.export.GAFExporter
 
getWrittenResultsCount() - Method in class org.intermine.bio.web.export.GFF3Exporter
getWrittenResultsCount() - Method in class org.intermine.bio.web.export.SequenceExporter
getWrittenResultsCount() - Method in interface org.intermine.web.logic.export.Exporter
 
getWrittenResultsCount() - Method in class org.intermine.web.logic.export.ExporterImpl
getXAxisLabel() - Method in class org.intermine.webservice.client.widget.Widget
 
getXml() - Method in class org.intermine.web.struts.ImportTagsForm
Get the xml.
getXml() - Method in class org.intermine.web.struts.ImportXMLForm
Get the xml.
getXML() - Method in class org.intermine.webservice.server.query.QueryUploadService
Get the XML which represents the queries to be saved.
getXml() - Method in class org.intermine.webservice.server.query.result.QueryResultInput
Gets xml query string.
getXMLSchemaUrl() - Method in class org.intermine.webservice.server.query.AbstractQueryService
 
getXref() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
 
getXrefs() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
used for testing
getXrefs() - Method in class org.intermine.bio.ontology.OboTerm
Get a set of xrefs (OboTerms) for this term.
getYAxisLabel() - Method in class org.intermine.webservice.client.widget.Widget
 
GFF3Converter - Class in org.intermine.bio.dataconversion
Class to read a GFF3 source data and produce a data representation
GFF3Converter(ItemWriter, String, String, String, String, Model, GFF3RecordHandler, GFF3SeqHandler) - Constructor for class org.intermine.bio.dataconversion.GFF3Converter
Constructor
GFF3ConverterTask - Class in org.intermine.bio.task
Task to convert gff3 data
GFF3ConverterTask() - Constructor for class org.intermine.bio.task.GFF3ConverterTask
 
GFF3Exporter - Class in org.intermine.bio.web.export
Exports LocatedSequenceFeature objects in GFF3 format.
GFF3Exporter(PrintWriter, List<Integer>, Map<String, String>, List<String>, String, Set<Integer>, boolean) - Constructor for class org.intermine.bio.web.export.GFF3Exporter
Constructor.
GFF3Exporter(PrintWriter, List<Integer>, Map<String, String>, List<String>, String, Set<Integer>, boolean, List<Path>) - Constructor for class org.intermine.bio.web.export.GFF3Exporter
Constructor.
GFF3ExportForm - Class in org.intermine.bio.web.struts
Form for sequence export (FASTA probably)
GFF3ExportForm() - Constructor for class org.intermine.bio.web.struts.GFF3ExportForm
 
GFF3HttpExporter - Class in org.intermine.bio.web.export
An implementation of TableHttpExporter that exports LocatedSequenceFeature objects in GFF3 format.
GFF3HttpExporter() - Constructor for class org.intermine.bio.web.export.GFF3HttpExporter
 
GFF3ListService - Class in org.intermine.bio.webservice
Export a List as GFF3.
GFF3ListService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.GFF3ListService
 
GFF3ListServlet - Class in org.intermine.bio.webservice
 
GFF3ListServlet() - Constructor for class org.intermine.bio.webservice.GFF3ListServlet
 
GFF3Parser - Class in org.intermine.bio.io.gff3
A parser for GFF3 files.
GFF3QueryServlet - Class in org.intermine.bio.webservice
A servlet to hand off to the GFF3-query-service.
GFF3QueryServlet() - Constructor for class org.intermine.bio.webservice.GFF3QueryServlet
 
GFF3Record - Class in org.intermine.bio.io.gff3
A class that represents one line of a GFF3 file.
GFF3Record(String) - Constructor for class org.intermine.bio.io.gff3.GFF3Record
Create a GFF3Record from a line of a GFF3 file
GFF3Record(String, String, String, int, int, Double, String, String, Map<String, List<String>>) - Constructor for class org.intermine.bio.io.gff3.GFF3Record
Create a new GFF3Record
GFF3RecordHandler - Class in org.intermine.bio.dataconversion
Permits specific operations to be performed when processing an line of GFF3.
GFF3RecordHandler(Model) - Constructor for class org.intermine.bio.dataconversion.GFF3RecordHandler
Construct with the model to create items in (for type checking).
GFF3SeqHandler - Class in org.intermine.bio.dataconversion
An interface used by GFF3Converter to choose the type of sequence Items.
GFF3SeqHandler() - Constructor for class org.intermine.bio.dataconversion.GFF3SeqHandler
 
GFF3Util - Class in org.intermine.bio.web.export
Utility methods for GFF3.
GFF_FIELDS - Static variable in class org.intermine.bio.web.export.GFF3Exporter
the fields we don't want to display as attributes
GFFQueryService - Class in org.intermine.bio.webservice
A service for exporting query results as gff3.
GFFQueryService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.GFFQueryService
Constructor.
GLOBAL - Static variable in class org.intermine.api.search.Scope
Global scope for public bags, templates, etc.
GLOBAL_BAGS - Static variable in class org.intermine.api.search.SearchTarget
The search target for global bags
GLOBAL_CACHE - Static variable in class org.intermine.web.logic.Constants
Servlet attribute.
GLOBAL_SEARCH_REPOSITORY - Static variable in class org.intermine.web.logic.Constants
Servlet attribute.
GLOBAL_SEGMENT - Static variable in class org.intermine.webservice.server.jbrowse.Segment
global segment
GLOBAL_TEMPLATES - Static variable in class org.intermine.api.search.SearchTarget
The search target for global templates
GlobalRepository - Class in org.intermine.api.search
A representation of an object that knows how to index global objects, and also how to respond to changes to those objects.
GlobalRepository(Profile) - Constructor for class org.intermine.api.search.GlobalRepository
Build a new global search repository and register it with the list of global repositories available.
GLOBALS - Static variable in class org.intermine.api.search.SearchRepository
 
GoConverter - Class in org.intermine.bio.dataconversion
DataConverter to parse a go annotation file into Items
GoConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.GoConverter
Constructor
goFaster() - Method in class org.intermine.api.results.ExportResultsIterator
Switches on the goFaster mode in the objectstore for this query.
goFaster() - Method in class org.intermine.api.results.WebResults
Calls ObjectStore.goFaster() if this object wraps a Results object from an ObjectStoreInterMineImpl.
goFaster(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Makes a certain Query go faster, using extra resources.
goFasterCacheMap - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
goFasterCountMap - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
goFasterMap - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
goFasterWithConnection(Query, Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Makes a certain Query go faster, using extra resources.
GoPostprocess - Class in org.intermine.bio.postprocess
Take any GOAnnotation objects assigned to proteins and copy them to corresponding genes.
GoPostprocess(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.GoPostprocess
Create a new UpdateOrthologes object from an ObjectStoreWriter
GORNULL - Static variable in class org.intermine.sql.query.Constraint
An operation for this constraint indicating that the left is greater than the right, or the left is null.
goTerms - Variable in class org.intermine.bio.dataconversion.GoConverter
 
GotoWebSearchableAction - Class in org.intermine.web.struts
Action handles search.
GotoWebSearchableAction() - Constructor for class org.intermine.web.struts.GotoWebSearchableAction
 
grant(Database, String, String) - Static method in class org.intermine.sql.DatabaseUtil
Grant permission on all tables for given user on specified database.
grantPermission(String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
Grant permission to the given identity, creating a profile for this identity if it is not already available.
GrantTask - Class in org.intermine.task
Task to grant permissions on all tables in a database to a given user.
GrantTask() - Constructor for class org.intermine.task.GrantTask
 
GRAPH_CACHE - Static variable in class org.intermine.web.logic.Constants
Servlet attribute.
GraphJSONProcessor - Class in org.intermine.webservice.server.widget
A widget result processor that produces chart results in JSON.
GraphService - Class in org.intermine.webservice.server.widget
 
GraphService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.GraphService
 
GraphWidget - Class in org.intermine.web.logic.widget
 
GraphWidget(GraphWidgetConfig, InterMineBag, ObjectStore, WidgetOptions) - Constructor for class org.intermine.web.logic.widget.GraphWidget
 
GraphWidget.DivNumberFormat - Class in org.intermine.web.logic.widget
class used to format the p-values on the graph
GraphWidget.DivNumberFormat(int) - Constructor for class org.intermine.web.logic.widget.GraphWidget.DivNumberFormat
 
GraphWidgetActionType - Enum in org.intermine.web.logic.widget
Enumeration for possible actions when create the query for graph widgets.
GraphWidgetConfig - Class in org.intermine.web.logic.widget.config
Configuration object describing details of a graph displayer
GraphWidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
GraphWidgetLoader - Class in org.intermine.web.logic.widget
The class that does the actual querying for results.
GraphWidgetLoader(InterMineBag, ObjectStore, GraphWidgetConfig, String) - Constructor for class org.intermine.web.logic.widget.GraphWidgetLoader
Constructor.
GraphWidgetsServlet - Class in org.intermine.webservice.server.widget
Servlet running WidgetsService.
GraphWidgetsServlet() - Constructor for class org.intermine.webservice.server.widget.GraphWidgetsServlet
 
GraphXMLProcessor - Class in org.intermine.webservice.server.widget
A processor for returning results from graph widgets in XML.
GraphXMLProcessor() - Constructor for class org.intermine.webservice.server.widget.GraphXMLProcessor
Constructor, obvs
GREATER - Static variable in class org.intermine.sql.query.AbstractValue
Describes one AbstractValue as being greater than another AbstractValue.
GREATER_THAN - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is greater than the second
GREATER_THAN_EQUALS - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is greater than or equal to the second
greaterOrEqual(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
Compare this value of this AbstractValue with another to see if it is more or equal.
greaterThan(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be greater than a value.
greaterThan(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
Compare this value of this AbstractValue with another to see if it is more.
greaterThanEqualTo(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be greater than or equal to a value.
GREATEST - Static variable in class org.intermine.objectstore.query.QueryExpression
Return the greatest value from two expressions, e.g.
GREATEST - Static variable in class org.intermine.sql.query.Function
GREATEST(x, y) - takes two operands
groupBy - Variable in class org.intermine.sql.query.Query
 
groupByClass(Collection<E>, boolean) - Static method in class org.intermine.util.CollectionUtil
Sorts objects in the given collection into different types by Class.
groupGenomicRegionByInterval(String, Set<GenomicRegion>) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchUtil
Look for genomic regions within or overlap an interval.

H

handleCreation(CreationEvent) - Method in class org.intermine.api.search.GlobalRepository
 
handleCreation(CreationEvent) - Method in class org.intermine.api.search.SearchRepository
Respond in some way to the creation of a web searchable object.
handleCreation(CreationEvent) - Method in class org.intermine.api.search.UserRepository
 
handleDeletion(DeletionEvent) - Method in class org.intermine.api.search.SearchRepository
Respond in some way to the deletion of a web searchable object.
handleDeletion(DeletionEvent) - Method in class org.intermine.api.search.UserRepository
 
handleErrorOutput(String) - Method in class org.intermine.task.SetDeployURL
 
handleErrorResponse() - Method in class org.intermine.webservice.client.util.HttpConnection
Handles an error response received while executing a service request.
handleHeaderAttributes(Map<String, Object>, StringBuilder) - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
handleHeaderAttributes(Map<String, Object>, StringBuilder) - Method in class org.intermine.webservice.server.output.XMLFormatter
Serialise the headers to the current string builder.
handleMassTagging() - Method in class org.intermine.api.search.GlobalRepository
 
handleMassTagging() - Method in class org.intermine.api.search.SearchRepository
Respond to the fact that multiple tags have been added and that we do not know what they are.
handleMassTagging() - Method in class org.intermine.api.search.UserRepository
 
handleMessages(BagQueryResult, HttpSession, Properties, String, String) - Static method in class org.intermine.web.struts.DisplayLookupMessageHandler
Generates and saves messages for bag lookup
handleOutput(String, int) - Method in class org.intermine.task.SetDeployURL
 
handleOutput(String) - Method in class org.intermine.task.SetDeployURL
 
handlePropertyChange(PropertyChangeEvent) - Method in class org.intermine.api.search.SearchRepository
Respond in some way to the change in the properties of a web searchable object.
handlePropertyChange(PropertyChangeEvent) - Method in class org.intermine.api.search.UserRepository
 
handlerClassName - Variable in class org.intermine.bio.task.GFF3ConverterTask
 
handleTagAddition(TaggingEvent) - Method in class org.intermine.api.search.GlobalRepository
 
handleTagAddition(TaggingEvent) - Method in class org.intermine.api.search.SearchRepository
Respond in some way to the addition of a tag to a web searchable object.
handleTagAddition(TaggingEvent) - Method in class org.intermine.api.search.UserRepository
 
handleTagRemoval(TaggingEvent) - Method in class org.intermine.api.search.GlobalRepository
 
handleTagRemoval(TaggingEvent) - Method in class org.intermine.api.search.SearchRepository
Respond in some way to the removal of a tag from a web searchable object.
handleTagRemoval(TaggingEvent) - Method in class org.intermine.api.search.UserRepository
 
HAS - Static variable in class org.intermine.metadata.ConstraintOp
Require that the left argument has at least one of the right argument.
hasAllTags(Taggable) - Method in class org.intermine.api.search.TagFilter
Check to see if this taggable item has all the tags it is meant to.
hasAttribute(String) - Method in class org.intermine.xml.full.Item
Return true if named attribute exists.
hasAutocompleter(String, String) - Method in class org.intermine.web.autocompletion.AutoCompleter
checks if an autocompletion exists
hasBioSeg - Variable in class org.intermine.objectstore.intermine.DatabaseSchema
 
hasBioSeg() - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns true if the database has the bioseg type installed.
hasCallback() - Method in class org.intermine.webservice.server.WebService
Determine whether a callback was supplied to this request.
hasClassDescriptor(String) - Method in class org.intermine.metadata.Model
Return true if named ClassDescriptor is found in the model.
hasClassName(String) - Method in class org.intermine.bio.dataconversion.IdResolver
Return true if the idResolver contains information about this class name.
hasCollection(String) - Method in class org.intermine.xml.full.Item
Return true if named collection exists.
hasComments() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
hasDatasetRefId() - Method in class org.intermine.bio.dataconversion.UniprotEntry
returns true if the protein has a dataset of SwissProt or Trembl.
HasFromList - Interface in org.intermine.objectstore.query
Interface to define the types of things that can have from elements added to them.
hashCode() - Method in class org.intermine.api.bag.BagQueryResult.IssueResult
hashCode() - Method in class org.intermine.api.bag.SharingInvite
 
hashCode() - Method in class org.intermine.api.beans.ObjectDetails
 
hashCode() - Method in class org.intermine.api.beans.PartnerLink
 
hashCode() - Method in class org.intermine.api.idresolution.ResolutionJob
 
hashCode() - Method in class org.intermine.api.mines.ObjectRequest
 
hashCode() - Method in class org.intermine.api.mines.RemoteMine
 
hashCode() - Method in class org.intermine.api.profile.BagValue
 
hashCode() - Method in class org.intermine.api.profile.SavedQuery
Hash code.
hashCode() - Method in class org.intermine.api.results.Column
hashCode() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
hashCode() - Method in class org.intermine.api.results.flatouterjoins.MultiRowLaterValue
hashCode() - Method in class org.intermine.api.results.ResultElement
hashCode() - Method in class org.intermine.api.template.ApiTemplate
 
hashCode() - Method in class org.intermine.bio.chado.ChadoCVTerm
hashCode() - Method in class org.intermine.bio.ontology.OboTermSynonym
hashCode() - Method in class org.intermine.bio.util.OrganismData
hashCode() - Method in class org.intermine.bio.web.model.GenomicRegion
 
hashCode() - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint
 
hashCode() - Method in class org.intermine.metadata.AttributeDescriptor
hashCode() - Method in class org.intermine.metadata.ClassDescriptor
hashCode() - Method in class org.intermine.metadata.CollectionDescriptor
hashCode() - Method in class org.intermine.metadata.Model
hashCode() - Method in class org.intermine.metadata.PrimaryKey
hashCode() - Method in class org.intermine.metadata.ReferenceDescriptor
hashCode() - Method in class org.intermine.metadata.StringUtil.LineWrappedString
hashCode(Object) - Static method in class org.intermine.metadata.Util
Return a zero hashCode if the object is null, otherwise return the real hashCode
hashCode() - Method in class org.intermine.objectstore.query.BagConstraint
hashCode() - Method in class org.intermine.objectstore.query.ClassConstraint
Get the hashCode for this object
hashCode() - Method in class org.intermine.objectstore.query.Clob
Override Object#hashCode.
hashCode() - Method in class org.intermine.objectstore.query.ConstraintSet
Get the hashCode for this object overrides Object.hashCode().
hashCode() - Method in class org.intermine.objectstore.query.ContainsConstraint
Get the hashCode for this object, overrides Object.hashCode()
hashCode() - Method in class org.intermine.objectstore.query.iql.IqlQuery
hashCode() - Method in class org.intermine.objectstore.query.MultipleInBagConstraint
hashCode() - Method in class org.intermine.objectstore.query.ObjectStoreBag
Override Object#hashCode.
hashCode() - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
hashCode() - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject
hashCode() - Method in class org.intermine.objectstore.query.OverlapConstraint
hashCode() - Method in class org.intermine.objectstore.query.PathExpressionField
hashCode() - Method in class org.intermine.objectstore.query.QueryCast
hashCode() - Method in class org.intermine.objectstore.query.QueryField
Returns a hash code for this object.
hashCode() - Method in class org.intermine.objectstore.query.QueryValue
Overrides Object.
hashCode() - Method in class org.intermine.objectstore.query.Results
 
hashCode() - Method in class org.intermine.objectstore.query.ResultsInfo
hashCode() - Method in class org.intermine.objectstore.query.SimpleConstraint
Get the hashCode for this object overrides Object.hashCode()
hashCode() - Method in class org.intermine.objectstore.query.SubqueryConstraint
Get the hashCode for this object overrides Object.hashCode()
hashCode() - Method in class org.intermine.objectstore.query.SubqueryExistsConstraint
Get the hashCode for this object overrides Object.hashCode()
hashCode() - Method in class org.intermine.pathquery.LogicExpression
hashCode() - Method in class org.intermine.pathquery.Node
hashCode() - Method in class org.intermine.pathquery.OrderElement
hashCode() - Method in class org.intermine.pathquery.Path
hashCode() - Method in class org.intermine.pathquery.PathQuery
 
hashCode() - Method in class org.intermine.sql.precompute.PrecomputedTable
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.AbstractConstraint
Overrides Object.hashcode();
hashCode() - Method in class org.intermine.sql.query.AbstractTable
Overrides Object.hashcode().
hashCode() - Method in class org.intermine.sql.query.AbstractValue
Overrides Object.hashcode().
hashCode() - Method in class org.intermine.sql.query.Constant
Overrides Object.hashcode().
hashCode() - Method in class org.intermine.sql.query.Constraint
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.ConstraintSet
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.ExplainResult
hashCode() - Method in class org.intermine.sql.query.Field
Overrides Object.hashcode().
hashCode() - Method in class org.intermine.sql.query.Function
Overrides Object.hashcode.
hashCode() - Method in class org.intermine.sql.query.InListConstraint
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.NotConstraint
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.OrderDescending
Overrides Object.hashcode().
hashCode() - Method in class org.intermine.sql.query.Query
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.SelectValue
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.SubQuery
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.SubQueryConstraint
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.Table
Overrides Object.hashcode().
hashCode() - Method in class org.intermine.sql.writebatch.Row
hashCode() - Method in class org.intermine.template.TemplateQuery
 
hashCode() - Method in class org.intermine.util.AlwaysMap
hashCode() - Method in class org.intermine.util.IdentityMap
hashCode() - Method in class org.intermine.util.ReferenceMap
hashCode() - Method in class org.intermine.web.logic.config.Displayer
hashCode() - Method in class org.intermine.web.logic.config.FieldConfig
hashCode() - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart
 
hashCode() - Method in class org.intermine.web.logic.config.TableExportConfig
hashCode() - Method in class org.intermine.web.logic.config.Type
hashCode() - Method in class org.intermine.web.logic.config.WebConfig
hashCode() - Method in class org.intermine.web.logic.template.ConstraintInput
 
hashCode() - Method in class org.intermine.web.logic.TreeNode
hashCode() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
 
hashCode() - Method in class org.intermine.webservice.client.results.Item
 
hashCode() - Method in class org.intermine.webservice.client.results.Page
 
hashCode() - Method in class org.intermine.webservice.server.core.Either
 
hashCode() - Method in class org.intermine.webservice.server.core.Either.Left
 
hashCode() - Method in class org.intermine.webservice.server.core.Either.Right
 
hashCode() - Method in class org.intermine.webservice.server.jbrowse.Command
 
hashCode() - Method in class org.intermine.webservice.server.jbrowse.Segment
 
hashCode() - Method in class org.intermine.webservice.server.JWTBuilder
 
hashCode() - Method in class org.intermine.xml.full.Attribute
hashCode() - Method in class org.intermine.xml.full.Item
hashCode() - Method in class org.intermine.xml.full.Reference
hashCode() - Method in class org.intermine.xml.full.ReferenceList
hashCodeNoUnion() - Method in class org.intermine.sql.query.Query
Returns a partial hashcode, ignoring other queries in the union.
hasHelperForType(Class<?>) - Static method in class org.intermine.api.query.MainHelper.RangeConfig
 
hashPassword(String) - Static method in class org.intermine.util.PasswordHasher
Converts a password into a hashed password, with a salt.
hasIssues() - Method in class org.intermine.web.logic.profile.ProfileMergeIssues
 
hasJBrowseTrack(String) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Test if jbrowse has a track regards to a feature type
hasKeyFields(Map<String, List<FieldDescriptor>>, String) - Static method in class org.intermine.api.config.ClassKeyHelper
For a given classreturn true if it has any identifying fields.
hasNext() - Method in class org.intermine.api.results.ExportResultsIterator
hasNext() - Method in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator
hasNext() - Method in class org.intermine.util.CombinedIterator
hasNext() - Method in class org.intermine.util.ObjectPipe
hasNext() - Method in class org.intermine.util.SynchronisedIterator
hasNext() - Method in class org.intermine.webservice.server.core.TableRowIterator
 
hasNext() - Method in class org.intermine.webservice.server.output.FilteringResultIterator
 
hasNext() - Method in class org.intermine.webservice.server.output.JSONDataTableRowIterator
 
hasNext() - Method in class org.intermine.webservice.server.output.JSONResultsIterator
hasNext() - Method in class org.intermine.webservice.server.output.JSONRowIterator
 
hasNext() - Method in class org.intermine.webservice.server.output.MinimalJsonIterator
 
hasPrimaryAccession() - Method in class org.intermine.bio.dataconversion.UniprotEntry
some proteins don't have accessions.
hasProblems() - Method in class org.intermine.metadata.Model
Return true if there are problems with the model despite it's successful creation.
hasProfile(String) - Method in class org.intermine.api.profile.ProfileManager
Check whether a user already has a Profile
hasReference(String) - Method in class org.intermine.xml.full.Item
Return true if named reference exists.
hasSeries() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
hasTag(String, Taggable) - Method in class org.intermine.api.profile.TagManager
Test whether a particular taggable thing has been tagged with a particular tag.
hasTag(String, Taggable, Profile) - Method in class org.intermine.api.profile.TagManager
Test whether a particular taggable thing has been tagged with a particular tag, by a particular user.
hasTaxon(String) - Method in class org.intermine.bio.dataconversion.IdResolver
Return true if the idResolver contains information about this taxon id.
hasTaxonAndClassName(String, String) - Method in class org.intermine.bio.dataconversion.IdResolver
Check if resolver has taxon id and class name
hasTaxonAndClassNames(String, Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver
Check if resolver has taxon id and class name
hasTaxons(Set<String>) - Method in class org.intermine.bio.dataconversion.IdResolver
Return true if the idResolver contains information about a collection of taxon id.
hasTaxonsAndClassName(Set<String>, String) - Method in class org.intermine.bio.dataconversion.IdResolver
Check if resolver has taxon id and class name
hasTaxonsAndClassNames(Map<String, Set<String>>) - Method in class org.intermine.bio.dataconversion.IdResolver
Check if resolver has a set of keys (taxon id + class name)
hasValidPath(Object, String, InterMineAPI) - Static method in class org.intermine.web.logic.WebUtil
Check whether the runtime type of an object supports a particular path.
having - Variable in class org.intermine.sql.query.Query
 
HeaderConfigLink - Class in org.intermine.web.logic.config
Will store a link configured through HeaderConfig (WebConfig) and used on report page header
HeaderConfigLink() - Constructor for class org.intermine.web.logic.config.HeaderConfigLink
 
HeaderConfigTitle - Class in org.intermine.web.logic.config
Configuration of an object (Type) header when displayed on report
HeaderConfigTitle() - Constructor for class org.intermine.web.logic.config.HeaderConfigTitle
 
HeaderConfigTitle.TitlePart - Class in org.intermine.web.logic.config
Holder for a path that appears in the title and any prefix and suffix values if they have been configured.
HeaderFilter - Class in org.intermine.web.filters
A Filter that modifies response headers of outgoing pages.
HeaderFilter() - Constructor for class org.intermine.web.filters.HeaderFilter
 
HeartbeatAction - Class in org.intermine.web.struts
Takes a parameter "type" with value "webapp" or "query" and prints "OK" to the client if everything is ok, otherwise something else.
HeartbeatAction() - Constructor for class org.intermine.web.struts.HeartbeatAction
 
HgncIdResolverFactory - Class in org.intermine.bio.dataconversion
Create an IdResolver for HGNC previous symbols and aliases to current symbols.
HgncIdResolverFactory() - Constructor for class org.intermine.bio.dataconversion.HgncIdResolverFactory
Construct without SO term of the feature type.
HIDDEN - Static variable in class org.intermine.web.logic.Constants
The preference set if the user does not want to be found
hideColumn(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction
Deprecated.
as we don't hide columns any more
HintingFetcher - Class in org.intermine.dataloader
Class providing EquivalentObjectFetcher functionality that makes use of hints to improve performance.
HintingFetcher(BaseEquivalentObjectFetcher) - Constructor for class org.intermine.dataloader.HintingFetcher
Constructor
HintManager - Class in org.intermine.web.logic.help
Hints are shown at the top of the pages in the web application, this class reads the hints in from properties and returns appropriate hints for a specified page.
HintManager(Properties) - Constructor for class org.intermine.web.logic.help.HintManager
Construct with the InterMine web properties, extract the configured hints and set up in an internal map.
HintsController - Class in org.intermine.web.struts
Executed for the hints tile that displays text information at the top of webapp pages.
HintsController() - Constructor for class org.intermine.web.struts.HintsController
 
HomologeneConverter - Class in org.intermine.bio.dataconversion
HomoloGene data converter, to use symbol and organism to identify a gene
HomologeneConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.HomologeneConverter
Constructor
HomologeneConverter.GeneRecord - Class in org.intermine.bio.dataconversion
represents a gene record in the data files
HomologeneConverter.GeneRecord(String, String) - Constructor for class org.intermine.bio.dataconversion.HomologeneConverter.GeneRecord
 
HomologueDisplayer - Class in org.intermine.bio.web.displayer
Displayer for Homology
HomologueDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.HomologueDisplayer
Construct with config information read from webconfig-model.xml and the API.
HtmlHeadController - Class in org.intermine.web.struts
Controller for the html head tile.
HtmlHeadController() - Constructor for class org.intermine.web.struts.HtmlHeadController
 
htmlId - Variable in class org.intermine.api.results.ResultElement
 
HtmlListFormatter - Class in org.intermine.webservice.server.lists
A formatter that represents lists as HTML.
HtmlListFormatter() - Constructor for class org.intermine.webservice.server.lists.HtmlListFormatter
 
HTMLOutput - Class in org.intermine.webservice.server.output
HTMLOutput extends is similar to MemoryOutput, only difference is, that it prints out errors immediately to output.
HTMLOutput(PrintWriter) - Constructor for class org.intermine.webservice.server.output.HTMLOutput
Constructor.
HTMLTableFormatter - Class in org.intermine.webservice.server.output
A formatter that presents query results as HTML.
HTMLTableFormatter() - Constructor for class org.intermine.webservice.server.output.HTMLTableFormatter
 
HTMLWidget - Class in org.intermine.web.logic.widget
Represents a widget with no data, it just diplays the "content" string.
HTMLWidget(WidgetConfig) - Constructor for class org.intermine.web.logic.widget.HTMLWidget
 
HTMLWidgetConfig - Class in org.intermine.web.logic.widget.config
dummy widget to output html widget
HTMLWidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.HTMLWidgetConfig
 
HttpClient - Class in org.intermine.web.util
Very simple http client that downloads data.
HttpClient() - Constructor for class org.intermine.web.util.HttpClient
 
HttpConnection - Class in org.intermine.webservice.client.util
The HttpConnection is class wrapping implementation details of http connection and the implementation can change easily.
HttpConnection(Request) - Constructor for class org.intermine.webservice.client.util.HttpConnection
 
HttpExporterBase - Class in org.intermine.web.logic.export.http
Abstract class with functionality common for all classes implementing TableHttpExporter interface like getting result from paged table.
HttpExporterBase() - Constructor for class org.intermine.web.logic.export.http.HttpExporterBase
 
HttpExportUtil - Class in org.intermine.web.logic.export.http
Util for export.
HttpRequester - Class in org.intermine.api.mines
A mine requester that makes HTTP requests.
HttpRequester() - Constructor for class org.intermine.api.mines.HttpRequester
Create an object that will make HTTP requests
HumanIdResolverFactory - Class in org.intermine.bio.dataconversion
Create an IdResolverFactory for human genes - tracking Ensembl ids, NCBI ids, HGNC ids, HGNC symbols.
HumanIdResolverFactory() - Constructor for class org.intermine.bio.dataconversion.HumanIdResolverFactory
Construct without SO term of the feature type.
HUNDRED - Static variable in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
 
hyperLinkNote(String) - Static method in class org.intermine.task.AcceptanceTestTask
Return a hyperlinked version of the given note.

I

ID_ONLY - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
IDs only
identifier - Variable in class org.intermine.bio.dataconversion.TreefamConverter.GeneHolder
 
IDENTIFIER_CONSTRAINT - Static variable in class org.intermine.api.config.Constants
constrain by object identifier
identifierToId(String) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Turn an item identifier into an object id.
identifierType - Variable in class org.intermine.bio.dataconversion.TreefamConverter.GeneHolder
 
IdentityMap<E> - Class in org.intermine.util
This is a dumb implementation of a Map.
idMap - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher
 
idMap - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
idMapOps - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
IdResolutionService - Class in org.intermine.webservice.server.idresolution
 
IdResolutionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.idresolution.IdResolutionService
Default constructor.
IdResolutionServlet - Class in org.intermine.webservice.server.idresolution
Route requests for ID resolution.
IdResolutionServlet() - Constructor for class org.intermine.webservice.server.idresolution.IdResolutionServlet
 
IDResolver - Class in org.intermine.api.idresolution
 
IdResolver - Class in org.intermine.bio.dataconversion
Hold data about primary identifiers and synonyms for a particular class in the data model and provide methods to resolved synonyms into corresponding primary identifier(s).
IdResolver() - Constructor for class org.intermine.bio.dataconversion.IdResolver
Construct and empty IdResolver
IdResolver(String) - Constructor for class org.intermine.bio.dataconversion.IdResolver
Construct and empty IdResolver
idResolverCachedFileName - Static variable in class org.intermine.bio.dataconversion.IdResolverFactory
 
IdResolverFactory - Class in org.intermine.bio.dataconversion
Create an IdResolver.
IdResolverFactory() - Constructor for class org.intermine.bio.dataconversion.IdResolverFactory
 
IdResolverService - Class in org.intermine.bio.dataconversion
A wrapper class to provide IdResolver service.
idToIdentifier(Integer) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Turn an object id into an item identifier.
idToNamespace - Variable in class org.intermine.dataconversion.ItemToObjectTranslator
 
IdUpgrader - Interface in org.intermine.api.bag
Bag object id upgrader - find old objects in a new ObjectStore.
ignore - Variable in class org.intermine.web.filters.SetCharacterEncodingFilter
Should a character encoding specified by the client be ignored?
ignore - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
ignoreCombination(Map<Class<?>, Set<Class<?>>>, Class<?>, Class<?>) - Static method in class org.intermine.bio.postprocess.OverlapUtil
Return true if the given class should be ignored when overlapping with the other given class.
ignoreDuplicates - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
ignoreDuplicates - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
ignoreDuplicates - Variable in class org.intermine.dataloader.XmlDataLoaderTask
 
ignoreNames - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
im - Variable in class org.intermine.web.displayer.ReportDisplayer
 
im - Variable in class org.intermine.web.logic.bag.BagConverter
 
im - Variable in class org.intermine.webservice.server.WebService
The configuration object.
IM_ASPECT_MISC - Static variable in class org.intermine.api.tag.TagNames
String used to tag objects by Miscellaneous aspect
IM_ASPECT_PREFIX - Static variable in class org.intermine.api.tag.TagNames
String used to tag objects by some aspect
IM_CONVERTER - Static variable in class org.intermine.api.tag.TagNames
String used to tag converter templates in the webapp.
IM_FAVOURITE - Static variable in class org.intermine.api.tag.TagNames
String used to tag favourite objects
IM_HIDDEN - Static variable in class org.intermine.api.tag.TagNames
String used to tag objects that should be hidden at jsp page
IM_PREFIX - Static variable in class org.intermine.api.tag.TagNames
Prefix common for all InterMine internal tags
IM_PUBLIC - Static variable in class org.intermine.api.tag.TagNames
Tag for pubic things (bags, templates).
IM_REPORT - Static variable in class org.intermine.api.tag.TagNames
String used to tag templates that should appear on report pages.
IM_SEARCH_RESULTS - Static variable in class org.intermine.api.tag.TagNames
templates to be displayed on search results page
IM_SUMMARY - Static variable in class org.intermine.api.tag.TagNames
String used to tag objects to appear in the summary section of the report page
IM_WIDGET - Static variable in class org.intermine.api.tag.TagNames
bag with background population for specific widget
immutable - Variable in class org.intermine.objectstore.query.Results
 
imObj - Variable in class org.intermine.api.results.ResultElement
 
IMPLIED_BY - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes one constraint as being implied by another constraint.
IMPLIES - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes one constraint as implying another constraint.
ImportQueriesAction - Class in org.intermine.web.struts
Imports query in XML format and forward user to the query builder.
ImportQueriesAction() - Constructor for class org.intermine.web.struts.ImportQueriesAction
 
ImportQueriesForm - Class in org.intermine.web.struts
Form bean representing query import form.
ImportQueriesForm() - Constructor for class org.intermine.web.struts.ImportQueriesForm
 
ImportTagsAction - Class in org.intermine.web.struts
Import tags.
ImportTagsAction() - Constructor for class org.intermine.web.struts.ImportTagsAction
 
ImportTagsForm - Class in org.intermine.web.struts
Form bean representing tags import form.
ImportTagsForm() - Constructor for class org.intermine.web.struts.ImportTagsForm
Creates a new instance of ImportTagsForm.
ImportXMLForm - Class in org.intermine.web.struts
Form bean representing a generic import form.
ImportXMLForm() - Constructor for class org.intermine.web.struts.ImportXMLForm
Construct a form.
IN - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is IN the second
in(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be IN a named bag.
INCOMPARABLE - Static variable in class org.intermine.sql.query.AbstractValue
Describes one AbstractValue as being incomparable to another AbstractValue.
IncompatibleTypes - Exception in org.intermine.api.bag.operations
 
IncompatibleTypes(MetaDataException) - Constructor for exception org.intermine.api.bag.operations.IncompatibleTypes
 
IncompatibleTypesException - Exception in org.intermine.api.bag
Exception thrown when given bags are of incompatible types, has methods to set and fetch the types.
IncompatibleTypesException(String) - Constructor for exception org.intermine.api.bag.IncompatibleTypesException
Constructs an IncompatibleBagTypesException with the specified detail message.
IncompatibleTypesException(Throwable) - Constructor for exception org.intermine.api.bag.IncompatibleTypesException
Constructs an IncompatibleBagTypesException with the specified nested throwable.
IncompatibleTypesException(String, Throwable) - Constructor for exception org.intermine.api.bag.IncompatibleTypesException
Constructs an IncompatibleBagTypesException with the specified detail message and nested throwable.
incrementHintCount(String) - Method in class org.intermine.web.logic.results.WebState
Increment the number of times a hint has been displayed.
indefiniteArticle(String) - Static method in class org.intermine.metadata.StringUtil
Return 'a' or 'an' according to first letter of the given article.
INDENT - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
INDENT - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
INDENT - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
 
INDENT - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
INDENT - Static variable in class org.intermine.codegen.JavaModelOutput
 
INDENT - Static variable in class org.intermine.objectstore.intermine.TorqueModelOutput
 
INDENT2 - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
INDENT3 - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
indentXmlSimple(String) - Static method in class org.intermine.util.XmlUtil
Apply some indentiation to some XML.
INDEPENDENT - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints as being independent.
index - Variable in class org.intermine.api.results.Column
 
INDEX_OF - Static variable in class org.intermine.objectstore.query.QueryExpression
Position of specified string in other specified string
indexes - Variable in class org.intermine.api.search.SearchRepository
 
indexOf(Object) - Method in class org.intermine.webservice.client.results.ResultRowList
 
indirections - Variable in class org.intermine.objectstore.intermine.TorqueModelOutput
 
IndirectionTableBatch - Class in org.intermine.sql.writebatch
A class representing all changes to be made to an SQL indirection table.
IndirectionTableBatch(String, String) - Constructor for class org.intermine.sql.writebatch.IndirectionTableBatch
Constructor for this class.
IndirectionTableBatch(String, String, Set<Row>) - Constructor for class org.intermine.sql.writebatch.IndirectionTableBatch
Constructor for dodgy temp table deleting stuff
inferExperimentType(Set<String>, String) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Work out an experiment type give the combination of protocols used for the submission.
info - Variable in class org.intermine.objectstore.query.ResultsBatches
 
informUserOfNewSharedBag(String, Profile, InterMineBag) - Method in class org.intermine.util.Emailer
Send a 'sharing list' message
InheritanceDotTask - Class in org.intermine.task
Task that creates a DOT file describing the inheritance tree of java classes in the classpath.
InheritanceDotTask() - Constructor for class org.intermine.task.InheritanceDotTask
 
inIds(String, Collection<Integer>) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be IN a collection of ids.
init(HttpServletRequest) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
To set globally used variables.
init() - Method in class org.intermine.bio.webservice.BioExportServlet
init() - Method in class org.intermine.objectstore.query.ClobAccess
Initialises the state of this object.
init(FilterConfig) - Method in class org.intermine.web.filters.ExpiresHeaderFilter
Initialise this Filter.
init(FilterConfig) - Method in class org.intermine.web.filters.HeaderFilter
Initialise this Filter.
init(FilterConfig) - Method in class org.intermine.web.filters.ReleaseEtagFilter
 
init(FilterConfig) - Method in class org.intermine.web.filters.SetCharacterEncodingFilter
Place this filter into service.
init(ServletConfig) - Method in class org.intermine.web.logic.login.OpenIDAuthenticator
 
init(ActionServlet, ModuleConfig) - Method in class org.intermine.web.struts.InitialiserPlugin
Init method called at Servlet initialisation
init() - Method in class org.intermine.webservice.server.core.ConfigurableWebServiceServlet
 
init() - Method in class org.intermine.webservice.server.core.RestfulServlet
 
init(FilterConfig) - Method in class org.intermine.webservice.server.filter.RequestSubClassFilter
 
init(ServletConfig) - Method in class org.intermine.webservice.server.idresolution.IdResolutionServlet
 
init() - Method in class org.intermine.webservice.server.lists.ListInput
Initialise this structure
initialise() - Method in class org.intermine.bio.web.struts.SequenceExportForm
Initialiser
initialise(InterMineAPI, Properties, WebConfig, ResourceOpener) - Static method in class org.intermine.web.context.InterMineContext
Set up the Context with everything it needs.
initialise() - Method in class org.intermine.web.struts.BagUploadConfirmForm
Initialise the form.
initialise() - Method in class org.intermine.web.struts.ChangeTableSizeForm
Initialiser
initialise() - Method in class org.intermine.web.struts.CSVExportForm
Initialiser
initialise() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
Initialiser
initialise() - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Initialiser
initialise() - Method in class org.intermine.web.struts.ModifyBagForm
Initialiser
initialise() - Method in class org.intermine.web.struts.ModifyQueryForm
Initialiser
initialise() - Method in class org.intermine.web.struts.ModifySuperUserForm
Initialiser
initialise() - Method in class org.intermine.web.struts.ModifyTemplateForm
Initialiser
initialise() - Method in class org.intermine.web.struts.SaveBagForm
Initialiser
initialise() - Method in class org.intermine.web.struts.TableExportForm
Initialiser
initialise() - Method in class org.intermine.web.struts.TriageBagForm
 
initialise() - Method in class org.intermine.web.struts.WidgetForm
Initialiser
initialiseCommonFeatures(Map<Integer, FeatureData>) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Initialise SequenceProcessor with features that have already been processed and put the same features data into a commonFeaturesMap that tracks features (e.g.
initialised - Variable in class org.intermine.objectstore.query.ResultsBatches
 
initialiseDelendumAccumulator(Set<String>, ListInput) - Method in class org.intermine.webservice.server.lists.ListMakerService
Initialise the accumulator that builds up the list of temporary lists to delete.
initialiseFeatureMap(Map<Integer, FeatureData>) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Initialise FeatureMap with features that have already been processed.
initialiseMapsForFile() - Method in class org.intermine.bio.dataconversion.GoConverter
Reset maps that don't need to retain their contents between files.
INITIALISER_KEY_ERROR - Static variable in class org.intermine.web.logic.Constants
Key for the initialiser error
InitialiserPlugin - Class in org.intermine.web.struts
Initialiser for the InterMine web application.
InitialiserPlugin() - Constructor for class org.intermine.web.struts.InitialiserPlugin
 
initKeywordSearch(InterMineAPI, String) - Static method in class org.intermine.api.lucene.KeywordSearch
loads or creates the lucene index
initSession(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Initialise a new session.
initState() - Method in class org.intermine.webservice.server.jbrowse.Config
 
initState() - Method in class org.intermine.webservice.server.jbrowse.Names
 
initState() - Method in class org.intermine.webservice.server.model.ModelService
 
initState() - Method in class org.intermine.webservice.server.path.PossibleValuesService
 
initState() - Method in class org.intermine.webservice.server.query.result.QueryResultService
 
initState() - Method in class org.intermine.webservice.server.VersionService
 
initState() - Method in class org.intermine.webservice.server.WebService
Subclasses can put initialisation here.
initUserProfileResources(ObjectStoreWriter) - Method in class org.intermine.api.InterMineAPI
Initialise parts of this object that require connection to a user-profile object store.
INLINE_TABLE_SIZE - Static variable in class org.intermine.web.logic.Constants
The name of the property to look up to find the maximum size of an inline table.
InlineList - Class in org.intermine.web.logic.results
 
InlineList(Set<Object>, String, Boolean, String, Integer) - Constructor for class org.intermine.web.logic.results.InlineList
Set a set ;) of Objects by turning them into InterMineObjects and then InlineListObjects
InlineListConfig - Class in org.intermine.web.logic.config
Represents an inline list to be shown on a Report page
InlineListConfig() - Constructor for class org.intermine.web.logic.config.InlineListConfig
 
InlineListObject - Class in org.intermine.web.logic.config
An individual InterMineObject wrapped in an InlineList Set
InlineListObject(InterMineObject, Object, Object) - Constructor for class org.intermine.web.logic.config.InlineListObject
Initialize
InlineResultsTable - Class in org.intermine.web.logic.results
An inline table created from a Collection This table has one object per row
InlineResultsTable(Collection<?>, Model, WebConfig, Map<String, List<FieldDescriptor>>, int, boolean, List<Class<?>>) - Constructor for class org.intermine.web.logic.results.InlineResultsTable
Construct a new InlineResultsTable object
InlineResultsTable(Collection<?>, Model, WebConfig, Map<String, List<FieldDescriptor>>, int, boolean, List<Class<?>>, String, FieldDescriptor) - Constructor for class org.intermine.web.logic.results.InlineResultsTable
Construct with parent type and a field descriptor.
InlineResultsTableRow - Class in org.intermine.web.logic.results
Provides a wrapper for a row of InlineTableResultElement
InlineResultsTableRow() - Constructor for class org.intermine.web.logic.results.InlineResultsTableRow
 
InlineTableResultElement - Class in org.intermine.web.logic.results
ResultElement used in an InlineResultsTable
InlineTableResultElement(FastPathObject, Path, FieldConfig, Boolean) - Constructor for class org.intermine.web.logic.results.InlineTableResultElement
Instantiate ResultElement while saving its FieldConfig
InlineTagEditorController - Class in org.intermine.web.struts
Controller for the inline tag editing tile
InlineTagEditorController() - Constructor for class org.intermine.web.struts.InlineTagEditorController
 
InListConstraint - Class in org.intermine.sql.query
A representation of a constraint where an AbstractValue is IN a list of constants.
InListConstraint(AbstractValue) - Constructor for class org.intermine.sql.query.InListConstraint
Constructor for InListConstraint object.
inputModelFile - Variable in class org.intermine.task.ModelMergerTask
 
insertCollectionField(String, String, String, String, String, String, boolean) - Method in class org.intermine.bio.postprocess.CreateReferences
Add a collection of objects of type X to objects of type Y by using a connecting class.
insertReferenceField(String, String, String, String, String, String) - Method in class org.intermine.bio.postprocess.CreateReferences
Add a reference to and object of type X in objects of type Y by using a connecting class.
insertReferences() - Method in class org.intermine.bio.postprocess.CreateReferences
Fill in missing references/collections in model by querying relations
INSTANCE - Static variable in class org.intermine.pathquery.PathQueryBinding
A single instance of this class
INSTANCE - Static variable in class org.intermine.template.xml.TemplateQueryBinding
A single instance of this class
instance() - Static method in class org.intermine.webservice.server.widget.EnrichmentJSONProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.EnrichmentXMLProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.FlatFileWidgetResultProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.FlatWidgetProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.GraphJSONProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.JSONWidgetProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.TableJSONProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.TableXMLProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.XMLWidgetProcessor
 
instances - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
instances - Static variable in class org.intermine.sql.precompute.PrecomputedTableManager
 
instantiate(String) - Static method in class org.intermine.metadata.TypeUtil
Deprecated.
This method is named incorrectly - use getTypeByName instead.
instantiate(String) - Static method in class org.intermine.metadata.Util
Returns the Class for a given name (promoting primitives to their container class)
instantiateObject(String, String) - Static method in class org.intermine.util.DynamicUtil
Create an outline business object from a class name and a list of interface names
INT_BAG_TABLE_NAME - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the table that holds the integer ObjectStoreBag elements.
Integrate - Class in org.intermine.task
A task that can read a project.xml file and run a data integration build.
Integrate() - Constructor for class org.intermine.task.Integrate
 
IntegrationWriter - Interface in org.intermine.dataloader
Define methods needed to deal with integration when writing to an ObjectStore.
integrationWriter - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
integrationWriter - Variable in class org.intermine.dataloader.XmlDataLoaderTask
 
IntegrationWriterAbstractImpl - Class in org.intermine.dataloader
Abstract implementation of ObjectStoreIntegrationWriter.
IntegrationWriterAbstractImpl(ObjectStoreWriter) - Constructor for class org.intermine.dataloader.IntegrationWriterAbstractImpl
Constructs a new instance of an IntegrationWriter
IntegrationWriterDataTrackingImpl - Class in org.intermine.dataloader
Priority-based implementation of IntegrationWriter.
IntegrationWriterDataTrackingImpl(ObjectStoreWriter, DataTracker) - Constructor for class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Constructs a new instance of IntegrationWriterDataTrackingImpl.
IntegrationWriterDataTrackingImpl(ObjectStoreWriter, DataTracker, Set<Class<?>>) - Constructor for class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Constructs a new instance of IntegrationWriterDataTrackingImpl.
IntegrationWriterFactory - Class in org.intermine.dataloader
Produce IntegrationWriters
intercept(Object, Method, Object[], MethodProxy) - Method in class org.intermine.util.DynamicBean
Intercept all method calls, and operate on Map.
IntergenicRegionUtil - Class in org.intermine.bio.postprocess
Methods for creating feature for intergenic regions.
IntergenicRegionUtil(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.IntergenicRegionUtil
Create a new IntergenicRegionUtil object that will operate on the given ObjectStoreWriter.
INTERMINE_API - Static variable in class org.intermine.web.logic.Constants
Key for the InterMine API object
INTERMINE_VERSION - Static variable in class org.intermine.web.logic.Constants
Current version of the InterMine code
InterMineAction - Class in org.intermine.web.struts
An InterMine specific version of Action.
InterMineAction() - Constructor for class org.intermine.web.struts.InterMineAction
 
InterMineAPI - Class in org.intermine.api
InterMineAPI provides access to manager objects for the main parts of an InterMine application: the production ObjectStore, the userprofile (via ProfileManager), template queries, bags and tags.
InterMineAPI() - Constructor for class org.intermine.api.InterMineAPI
Protected no-argument constructor only used for building test implementations of this class.
InterMineAPI(ObjectStore, ObjectStoreWriter, ClassKeys, BagQueryConfig, ObjectStoreSummary, TrackerDelegate, LinkRedirectManager) - Constructor for class org.intermine.api.InterMineAPI
Construct an InterMine API object.
InterMineBag - Class in org.intermine.api.profile
An object that represents a bag of objects in our database for the webapp.
InterMineBag(String, String, String, Date, BagState, ObjectStore, Integer, ObjectStoreWriter, List<String>) - Constructor for class org.intermine.api.profile.InterMineBag
Constructs a new InterMineIdBag, and saves it in the UserProfile database.
InterMineBag(String, String, String, Date, BagState, ObjectStore, ObjectStoreWriter, List<String>) - Constructor for class org.intermine.api.profile.InterMineBag
Constructs a new InterMineBag, and saves it in the UserProfile database.
InterMineBag(ObjectStore, Integer, ObjectStoreWriter) - Constructor for class org.intermine.api.profile.InterMineBag
Loads an InterMineBag from the UserProfile database.
InterMineBag(ObjectStore, Integer, ObjectStoreWriter, boolean) - Constructor for class org.intermine.api.profile.InterMineBag
Loads an InterMineBag from the UserProfile database.
InterMineBagBinding - Class in org.intermine.api.xml
Parse InterMineIdBags in XML format
InterMineBagBinding() - Constructor for class org.intermine.api.xml.InterMineBagBinding
 
InterMineBagHandler - Class in org.intermine.api.xml
A handler for turning XML bags data into an InterMineIdBag.
InterMineBagHandler(ObjectStoreWriter, ObjectStoreWriter, Map<String, InterMineBag>, Map<String, InvalidBag>, Map<String, Set<BagValue>>, Integer) - Constructor for class org.intermine.api.xml.InterMineBagHandler
Create a new InterMineBagHandler object.
InterMineBagHandler(ObjectStoreWriter, ObjectStoreWriter, Map<String, InterMineBag>, Map<String, InvalidBag>, Map<String, Set<BagValue>>) - Constructor for class org.intermine.api.xml.InterMineBagHandler
Create a new InterMineBagHandler object.
InterMineContext - Class in org.intermine.web.context
A context object that doesn't require the session.
InterMineDispatchAction - Class in org.intermine.web.struts
An InterMine specific version of DispatchAction.
InterMineDispatchAction() - Constructor for class org.intermine.web.struts.InterMineDispatchAction
 
InterMineException - Exception in org.intermine
An Exception that may be thrown by client facing parts of InterMine code.
InterMineException() - Constructor for exception org.intermine.InterMineException
Constructs an InterMineException
InterMineException(String) - Constructor for exception org.intermine.InterMineException
Constructs an InterMineException with the specified detail message.
InterMineException(Throwable) - Constructor for exception org.intermine.InterMineException
Constructs an InterMineException with the specified nested throwable.
InterMineException(String, Throwable) - Constructor for exception org.intermine.InterMineException
Constructs an InterMineException with the specified detail message and nested throwable.
InterMineExceptionHandler - Class in org.intermine.web.struts
InterMine implementation of the Struts ExceptionHandler
InterMineExceptionHandler() - Constructor for class org.intermine.web.struts.InterMineExceptionHandler
 
InterMineFastPathObject - Interface in org.intermine.model
A root interface for all objects that can be stored in a InterMine database.
InterMineLinkGenerator - Interface in org.intermine.web.displayer
Helper class for intermine links generated on report and list pages
InterMineLinkGenerator - Class in org.intermine.web.util
Helper class for intermine links generated on report and list pages
InterMineLinkGenerator() - Constructor for class org.intermine.web.util.InterMineLinkGenerator
 
InterMineLookupDispatchAction - Class in org.intermine.web.struts
An InterMine specific version of LookupDispatchAction.
InterMineLookupDispatchAction() - Constructor for class org.intermine.web.struts.InterMineLookupDispatchAction
 
InterMineModelParser - Class in org.intermine.metadata
Parse InterMine metadata XML to produce an InterMine Model
InterMineModelParser() - Constructor for class org.intermine.metadata.InterMineModelParser
 
InterMineObject - Interface in org.intermine.model
A root interface for all objects that can be stored in a InterMine database.
InterMineObjectFetcher - Class in org.intermine.api.lucene
thread to fetch all intermineobjects (with exceptions) from database, create a lucene document for them, add references (if applicable) and put the final document in the indexing queue
InterMineObjectFetcher(ObjectStore, Map<String, List<FieldDescriptor>>, ObjectPipe<Document>, Set<Class<? extends InterMineObject>>, Map<Class<? extends InterMineObject>, Set<String>>, Map<Class<? extends InterMineObject>, String[]>, Map<ClassDescriptor, Float>, Vector<KeywordSearchFacetData>, Map<String, String>) - Constructor for class org.intermine.api.lucene.InterMineObjectFetcher
initialize the documentfetcher thread
InterMineRequestProcessor - Class in org.intermine.web.struts
A RequestProcessor that sends you back to the start if your session isn't valid.
InterMineRequestProcessor() - Constructor for class org.intermine.web.struts.InterMineRequestProcessor
 
InternalBagOperationException - Exception in org.intermine.api.bag.operations
Exceptions that are the fault of underlying infrastructure, and not the way the classes themselves were used. ie.
InternalBagOperationException() - Constructor for exception org.intermine.api.bag.operations.InternalBagOperationException
Constructor
InternalBagOperationException(String) - Constructor for exception org.intermine.api.bag.operations.InternalBagOperationException
 
InternalBagOperationException(Throwable) - Constructor for exception org.intermine.api.bag.operations.InternalBagOperationException
 
InternalBagOperationException(String, Throwable) - Constructor for exception org.intermine.api.bag.operations.InternalBagOperationException
 
internalCompare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.ConstraintSet
Compare this ConstraintSet with another AbstractConstraint, ignoring aliases in member fields and tables.
InternalErrorException - Exception in org.intermine.webservice.client.exceptions
The InternalErrorException is thrown by service when an error occurred at the server.
InternalErrorException(String) - Constructor for exception org.intermine.webservice.client.exceptions.InternalErrorException
 
InternalErrorException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.InternalErrorException
 
InternalErrorException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.InternalErrorException
 
InternalErrorException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.InternalErrorException
 
internalGetObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Internal service method for getObjectById.
internalGetObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Internal service method for getObjectById.
internalGetObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Internal service method for getObjectById.
internalGetObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Internal service method for getObjectById.
internalGetObjectByIdWithConnection(Connection, Integer, Class<?>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets an object by id given a Connection.
interpretFormat(String) - Static method in class org.intermine.webservice.server.WebServiceRequestParser
Figure out which format the user wants.
InterProConverter - Class in org.intermine.bio.dataconversion
DataConverter to parse InterPro data into items
InterProConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.InterProConverter
Constructor
InterproGoConverter - Class in org.intermine.bio.dataconversion
Loads go annotation from interpro2go goa file
InterproGoConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.InterproGoConverter
Constructor
INTERSECT - Static variable in class org.intermine.api.bag.BagOperations
Constant representing logical intersection.
intersect(Model, Collection<InterMineBag>, String, Profile, ClassKeys) - Static method in class org.intermine.api.bag.BagOperations
Create a bag that is the INTERSECTION of all the bags provided, if the intersection is the empty set then don't create the new bag.
INTERSECT - Static variable in class org.intermine.objectstore.query.ObjectStoreBagCombination
Constant representing an INTERSECTION operation
intersect(ItemList...) - Method in class org.intermine.webservice.client.services.ListService
Intersect one or more lists to produce a new list.
intersect(ListService.ListOperationInfo, ItemList...) - Method in class org.intermine.webservice.client.services.ListService
Intersect one or more lists to produce a new list.
intersect(Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService
Intersect one or more lists to produce a new list.
intersect(ListService.ListOperationInfo, Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService
Intersect one or more lists to produce a new list.
Intersection - Class in org.intermine.api.bag.operations
 
Intersection(Model, Profile, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.Intersection
 
IntHelper - Class in org.intermine.api.query.range
 
IntHelper() - Constructor for class org.intermine.api.query.range.IntHelper
 
IntPresentSet - Class in org.intermine.util
This is a set of ints.
IntPresentSet() - Constructor for class org.intermine.util.IntPresentSet
Constructor for this class.
intronMap - Variable in class org.intermine.bio.postprocess.IntronUtil
 
intronTranscripts - Variable in class org.intermine.bio.postprocess.IntronUtil
 
IntronUtil - Class in org.intermine.bio.postprocess
Methods for creating feature for introns.
IntronUtil(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.IntronUtil
Create a new IntronUtil object that will operate on the given ObjectStoreWriter.
IntToIntMap - Class in org.intermine.util
This is a map that maps from int to int.
IntToIntMap() - Constructor for class org.intermine.util.IntToIntMap
Constructor for this class.
INVALID_NAME_MSG - Static variable in class org.intermine.api.profile.TagManager
What we tell users when they give us an invalid tag name
INVALID_NAME_MSG - Static variable in class org.intermine.api.util.NameUtil
error message for bad names.
INVALID_QUERY - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
invalidate() - Method in class org.intermine.api.profile.InterMineBag
Declare that this bag is invalid, and return its InvalidBag representation.
invalidateBagTable(HttpSession, String) - Static method in class org.intermine.web.logic.session.SessionMethods
Remove a cached bag table from the session.
invalidateObjectById(Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Removes an entry from the objectstore getObjectById cache.
invalidateObjectById(Integer) - Method in interface org.intermine.objectstore.ObjectStore
Removes an entry from the objectstore getObjectById cache.
invalidateObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Removes an entry from the objectstore getObjectById cache.
invalidateObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Removes an entry from the objectstore getObjectById cache.
InvalidBag - Class in org.intermine.api.profile
A class representing a bag that is invalid because it does not conform to the current model.
InvalidBag(String, String, String, Date, ObjectStore, Integer, Integer, ObjectStoreBag, ObjectStoreWriter) - Constructor for class org.intermine.api.profile.InvalidBag
Constructor.
InvalidBag(String, String, String, Date, ObjectStore, ObjectStoreWriter) - Constructor for class org.intermine.api.profile.InvalidBag
Minimal constructor.
InvalidBag(SavedBag, Integer, ObjectStore, ObjectStoreWriter) - Constructor for class org.intermine.api.profile.InvalidBag
Constructor callable by the ProfileManager.
InvalidQueryException - Exception in org.intermine.api.query.codegen
A class representing a failure to generate the code for a query because the query is invalid.
InvalidQueryException(String) - Constructor for exception org.intermine.api.query.codegen.InvalidQueryException
Construct an exception with a single problem.
InvalidQueryException(Collection<? extends String>) - Constructor for exception org.intermine.api.query.codegen.InvalidQueryException
Construct an exception with a list of problems.
InvitationAction - Class in org.intermine.web.struts
Action that processes invitations.
InvitationAction() - Constructor for class org.intermine.web.struts.InvitationAction
 
InvitationForm - Class in org.intermine.web.struts
A form that contains the information for requests that invite users to share resources.
InvitationForm() - Constructor for class org.intermine.web.struts.InvitationForm
 
InvitationHandler - Class in org.intermine.api.bag
 
InvitationHandler() - Constructor for class org.intermine.api.bag.InvitationHandler
 
inviteToShare(InterMineBag, String) - Static method in class org.intermine.api.bag.SharedBagManager
Generate an invitation to share a bag.
invokeConstructor(ClobAccess) - Method in class org.intermine.objectstore.query.ClobAccess.ClobAccessSubclassFactory
Method to return a new instance of the subclass of ClobAccess that this object represents.
IqlQuery - Class in org.intermine.objectstore.query.iql
OQL representation of an object-based Query
IqlQuery() - Constructor for class org.intermine.objectstore.query.iql.IqlQuery
No-arg constructor (for deserialization)
IqlQuery(String, String, List<?>) - Constructor for class org.intermine.objectstore.query.iql.IqlQuery
Construct an IQL query from a String.
IqlQuery(String, String) - Constructor for class org.intermine.objectstore.query.iql.IqlQuery
Construct an IQL query from a String.
IqlQuery(Query) - Constructor for class org.intermine.objectstore.query.iql.IqlQuery
Construct an IQL query from a Query object.
IqlQueryParser - Class in org.intermine.objectstore.query.iql
Parser for the InterMine dialect of OQL (IQL)
IS_EMPTY - Static variable in class org.intermine.metadata.ConstraintOp
Synonym for IS NULL
IS_NOT_EMPTY - Static variable in class org.intermine.metadata.ConstraintOp
Synonym for IS NOT NULL
IS_NOT_NULL - Static variable in class org.intermine.metadata.ConstraintOp
Require that the argument is not null
IS_NULL - Static variable in class org.intermine.metadata.ConstraintOp
Require that the argument is null
IS_SUPERUSER - Static variable in class org.intermine.web.logic.Constants
Session attribute equals Boolean.TRUE when logged in user is superuser.
ISA - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument be of the type named by the right argument
isa(String) - Method in class org.intermine.webservice.client.results.Item
Determine whether this item belongs to the class of objects of the named type.
isAggregate() - Method in class org.intermine.sql.query.AbstractValue
Returns true if this value is an aggregate function.
isAggregate() - Method in class org.intermine.sql.query.Constant
Returns true if this value is an aggregate function.
isAggregate() - Method in class org.intermine.sql.query.Field
Returns true if this value is an aggregate function.
isAggregate() - Method in class org.intermine.sql.query.Function
Returns true if this value is an aggregate function.
isAggregate() - Method in class org.intermine.sql.query.OrderDescending
Returns true if this value is an aggregate function.
isAllRowsSelected() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return true if a whole column is selected either by selecting the whole column checkbox or by selecting each row individually.
isAnyBagInState(Profile, BagState) - Method in class org.intermine.api.bag.BagManager
Return true if there is at least one user bag for the given profile in the given state
isAnyBagInStates(Profile, Set<BagState>) - Method in class org.intermine.api.bag.BagManager
Return true if there is at least one user bag for the given profile in at least one of the given states
isAnyBagNotCurrent(Profile) - Method in class org.intermine.api.bag.BagManager
Return true if there is at least one user bag for the given profile in the 'not_current' state.
isAnyBagNotCurrentOrUpgrading(Profile) - Method in class org.intermine.api.bag.BagManager
Return true if there is at least one user bag for the given profile in the 'not_current' state or 'upgrading'.
isAnyBagToUpgrade(Profile) - Method in class org.intermine.api.bag.BagManager
Return true if there is at least one user bag for the given profile in the 'to_upgrade' state.
isAnyBagUnresolvable() - Method in class org.intermine.webservice.server.core.ListManager
Return true if there is at least one bag in the 'to_upgrade' state.
isApplicable() - Method in class org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient
Return true if the correction coefficient is applicable
isApplicable() - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient
Return true if the correction coefficient is applicable
isAspectTag(String) - Static method in class org.intermine.api.tag.AspectTagUtil
 
isAssignableFrom(Class<?>, Class<?>) - Static method in class org.intermine.util.DynamicUtil
Returns true if sup is a superclass of sub (or the same), taking into account dynamic classes.
isAssociatedWith(Constraint, FromElement) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Returns true if the constraint is associated with the given FromElement.
isAssociatedWithNothing(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Returns true if the given constraint is associated with no particular FromElement.
isAttribute() - Method in class org.intermine.metadata.FieldDescriptor
Is this FieldDescriptor an attribute?
isAttribute() - Method in class org.intermine.pathquery.Node
Gets the value of attribute
isAttribute() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns true if the path represents an attribute (rather than a class, reference, or collection).
isAuthenticated() - Method in class org.intermine.bio.webservice.AbstractRegionExportService
 
isAuthenticated() - Method in class org.intermine.webservice.server.WebService
 
isAuthorized() - Method in class org.intermine.webservice.client.lists.ItemList
 
isBagConstraint() - Method in class org.intermine.template.TemplateValue
Return true if this constraint value is a bag.
isBagSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing constraint and a bag has been selected.
isBagValuesEmpty(Connection) - Static method in class org.intermine.sql.DatabaseUtil
Verify if 'bagvalues' table is empty
isBoolean() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing having the attribute type boolean or Boolean
isCancelled() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Find out whether the query was cancelled.
isCancelledWithError() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Find out whether an error occured while trying to run the query.
isCellValidForPath(ResultElement, Path) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Test whether a result element matches the type of its path.
isChart() - Method in class org.intermine.webservice.client.widget.Widget
 
isCollection() - Method in class org.intermine.metadata.FieldDescriptor
Is this FieldDescriptor a collection?
isCollection() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns true if the reference is a collection.
isCollection() - Method in class org.intermine.pathquery.Node
Gets the value of collection
isCollection() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns true if the path represents a collection.
isComplement(String) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask
Return true if and only if the given location string represents a location on the reverse strand.
isCompleted() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Find out whether the query has completed.
isComputeTotalCount() - Method in class org.intermine.webservice.server.query.result.QueryResultInput
Returns true if should be displayed total count of all available results.
isConsistentType() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
 
isCountRequest(HttpServletRequest) - Static method in class org.intermine.webservice.server.WebServiceRequestParser
 
isCrossReference(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Returns true if the Constraint is a cross-reference between two QueryClasses.
isCurrent() - Method in class org.intermine.api.profile.InterMineBag
Return true if the status bag is current, otherwise false (status is not current or to upgrade)
isDeleteTracks() - Method in class org.intermine.web.struts.TemplatesImportForm
Get the deleteTracks flag.
isDirect() - Method in class org.intermine.bio.ontology.OboRelation
 
isDirty() - Method in class org.intermine.dataloader.ObjectDescription
Returns whether this ObjectDescription is dirty.
isDisabled() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if the constraint is disabled, false if it is enabled or locked.
isDistinct() - Method in class org.intermine.objectstore.query.Query
Get the value of the distinct property
isDistinct() - Method in class org.intermine.sql.query.Query
Gets the current distinct status of this query.
isDuplicate() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
isDuplicates - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
 
isEditable(PathConstraint) - Method in class org.intermine.template.TemplateQuery
Returns whether a constraint is editable.
isEditable() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Get the editable flag (when building a template).
isEditableInTemplate() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing template constraint and that constraint is editable.
isEditableInTemplate() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
Returns true if the constraint is part of a template query and the constraint is editable in that template.
isEdited() - Method in class org.intermine.template.TemplateQuery
Returns true if the TemplateQuery has been edited by the user and is therefore saved only in the query history.
isEmpty() - Method in class org.intermine.objectstore.query.Results
isEmpty(boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches
Returns true is there are no rows in the results.
isEmpty() - Method in class org.intermine.pathquery.PathQuery
Returns true if the query has no features yet.
isEmpty() - Method in class org.intermine.util.AlwaysMap
isEmpty() - Method in class org.intermine.util.IdentityMap
isEmpty() - Method in class org.intermine.util.PseudoSet
isEmpty() - Method in class org.intermine.util.ReferenceMap
isEmpty() - Method in class org.intermine.web.logic.results.DisplayField
Return true if the collection is empty or reference null.
isEmpty() - Method in class org.intermine.webservice.client.results.ResultRowList
 
isEmptyFeature(Map<GenomicRegion, List<List<String>>>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Check whether the results have empty features. for GenomicRegionSearchAjaxAction use.
isEmptyResultSet() - Method in class org.intermine.bio.dataconversion.EnsemblSnpDbConverter
For unit test perpose, when result set is empty, set to true
isEmptySelection() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return true if and only if nothing is selected
isEnabled() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if the constraint is enabled, false if it is disabled or locked.
isEnrichment() - Method in class org.intermine.webservice.client.widget.Widget
 
isErrorOnInitialiser(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Return true if exists blocking errors
isExplain() - Method in class org.intermine.sql.query.Query
Gets the current explain status of this query.
isExtraConstraint() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if this is a LOOKUP constraint and an extra constraint should be available.
isFailOnError() - Method in class org.intermine.task.SetDeployURL
 
isFetchFromInterMineObject() - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns true if ProxyReferences can be fetched from the InterMineObject table.
isFilterConstraint(WidgetConfig, PathConstraint) - Static method in class org.intermine.web.logic.widget.config.WidgetConfigUtil
 
isFirstPage() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Check if were are on the first page
isFlatMode(Class<?>) - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns true if the ObjectStore needs to run in flat mode for this Class - if notXml is missing and the InterMineObject table is missing (or if the class is not a subclass of InterMineObject).
isForcedInnerJoin() - Method in class org.intermine.web.logic.querybuilder.SummaryPath
Return true if this path is forced to be an inner join because it is involved in a loop constraint.
isFragment() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
isGeneratedClassAvailable(String) - Method in class org.intermine.metadata.Model
 
isGeneratedClassesAvailable() - Method in class org.intermine.metadata.Model
 
isGzip() - Method in class org.intermine.webservice.server.WebService
 
isInputFieldDisplayed() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if the input field can be displayed, method for use in JSP
isInRole(String) - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
True if the permission granted includes access to this role.
isInstance(Model, InterMineObject, String) - Static method in class org.intermine.bio.postprocess.PostProcessUtil
Convenience method to test whether an InterMineObject is an instance of the given class name without needing to import the class itself.
isInstance(Object, Class<?>) - Static method in class org.intermine.util.DynamicUtil
Returns true if obj is an instance of clazz, taking into account dynamic classes.
isInstanceOf(FastPathObject, String) - Static method in class org.intermine.metadata.TypeUtil
Return true if and only if the object is an instance of the class given by the className.
isInterbase() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
 
isInterface() - Method in class org.intermine.metadata.ClassDescriptor
True if this class is an interface.
isInTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Check whether the ObjectStore is performing a transaction, delegate to internal ObjectStoreWriter.
isInTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Check whether the ObjectStoreWriter is performing a transaction
isInTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter
Check whether the ObjectStoreWriter is performing a transaction
isInTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Finds if we are in a transaction.
isInvalidTemplate(WebSearchable) - Static method in class org.intermine.api.search.SearchResults
Check if a websearchable is an invalid template.
isIsoform() - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
isIssues() - Method in class org.intermine.web.struts.DisplayLookupMessageHandler
Check if there are any identifiers that didn't match.
isJBrowseEnabled() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Test if jbrowse is enabled
isJsonP(HttpServletRequest) - Static method in class org.intermine.webservice.server.WebServiceRequestParser
Work out if this a JSON-P request.
isKeyField(Map<String, List<FieldDescriptor>>, String, String) - Static method in class org.intermine.api.config.ClassKeyHelper
For a given class/field return true if it is an 'identifying' field.
isKeyField() - Method in interface org.intermine.api.results.ResultCell
 
isKeyField() - Method in class org.intermine.api.results.ResultElement
Return true if this object represents a field that is an identifying field (according to ClassKeyHelper.isKeyField())
isKeyField() - Method in class org.intermine.webservice.server.core.TableCell
 
isLastPage() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Check if we are on the last page
isLeaf() - Method in class org.intermine.web.logic.TreeNode
Is this node a leaf?
isLegalColumnName(String) - Static method in class org.intermine.sql.DatabaseUtil
Check that a column name provided to us is a legal column name, to prevent SQL injection.
isListConstraint(PathConstraint) - Static method in class org.intermine.web.logic.widget.config.WidgetConfigUtil
 
isListPathSet() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
isLocal() - Method in class org.intermine.api.profile.Profile
Returns true if this is a local account, and not, for example, an OpenID account.
isLocation() - Method in class org.intermine.task.project.UserProperty
Return true if and only if the location is set
isLocked() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if the constraint is locked, it should'n be enabled or disabled.
isLocked() - Method in class org.intermine.web.logic.querybuilder.SummaryPath
Return true if this path is locked because it is involved in a loop constraint.
isLoggedIn() - Method in class org.intermine.api.profile.Profile
Return true if and only if the user is logged is (and the Profile will be written to the userprofile).
isLoggedIn() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
isLoggedIn() - Method in class org.intermine.api.util.AnonProfile
 
isLookup() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if this constraint should be a LOOKUP, true if constraining a class (ref/col) instead of an attribute and that class has class keys defined.
isLoopSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing constraint and a loop value has been selected.
isMissingNotXml() - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns true if NotXML should be omitted from all tables except the InterMineObject table, and the InterMineObject table is present.
isMultiConnection() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.
isMultiConnection() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.
isMultiConnection() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.
isMultiConnection() - Method in interface org.intermine.objectstore.ObjectStore
Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.
isMultiConnection() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.
isMultiConnection() - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.
isMultipleValue() - Method in class org.intermine.template.TemplateValue
 
isMultiValue() - Method in class org.intermine.webservice.client.template.TemplateParameter
 
isMultiValuesDisplayed() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if the multi-select containing the possibleValue can be displayed, method for use in JSP
isMultiValueSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing constraint and a multivalue has been selected.
isNextEnabled() - Method in class org.intermine.web.tags.table.NavigationBarTag
 
isNotNull(String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be not null.
ISNT - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument be of the type named by the right argument
isNull(String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be null.
isNullSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing constraint and 'has a value' or 'has no value' has been selected.
isNumeric() - Method in class org.intermine.metadata.AttributeDescriptor
Returns true if the type of the attribute is some kind of number.
ISO8601DateFormat - Class in org.intermine.webservice.server.core
A date formatter for the ISO8601 date format.
ISO8601DateFormat() - Constructor for class org.intermine.webservice.server.core.ISO8601DateFormat
Constructor.
ISO_DATE_FORMAT - Static variable in class org.intermine.pathquery.ConstraintValueParser
A date format for ISO dates.
isObjectConstraint() - Method in class org.intermine.template.TemplateValue
Return true if this constraint value is on InterMineObject
isObsolete() - Method in class org.intermine.bio.ontology.OboTerm
Return the obsolete flag for this term.
isOfType(String) - Method in class org.intermine.api.profile.InterMineBag
Test whether the given type can be added to this bag, type can be a qualified or un-qualified string.
isOnlyAttribute() - Method in class org.intermine.pathquery.Path
Return true if the Path does not contain references or collections
isOpen() - Method in class org.intermine.web.logic.TreeNode
Is this node expanded?
isOpenByDefault() - Method in class org.intermine.web.logic.config.FieldConfig
Get whether this field should be uncollapsed if sectionOnRight is true.
isOpened() - Method in class org.intermine.webservice.client.util.HttpConnection
 
isOptional(PathConstraint) - Method in class org.intermine.template.TemplateQuery
Returns whether a constraint is optional.
isOuterJoin() - Method in class org.intermine.pathquery.Node
Returns true if this should be an outer join.
isOverlapped(GenomicRegion) - Method in class org.intermine.bio.web.model.GenomicRegion
Test if two regions are overlapped.
isOverwriting() - Method in class org.intermine.web.struts.ImportTagsForm
Get the overwrite flag.
isOverwriting() - Method in class org.intermine.web.struts.TemplatesImportForm
Get the overwrite flag.
isPathCompletelyInner(String) - Method in class org.intermine.pathquery.PathQuery
Returns true if a path string is in the root outer join group of this query.
isPathContainingSubClass(Model, String) - Static method in class org.intermine.web.logic.widget.config.WidgetConfigUtil
Check to see if the path contains a subclass.
isPossibleValuesDisplayed() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if the drop-down containing the possibleValues can be displayed, method for use in JSP
isPrecomputed(Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Checks if a query is precomputed or not for the given type
isPrecomputedWithConnection(Connection, Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Checks if a query is precomputed or not for the given type and connection
isPrimaryIdentifier(String, String, String) - Method in class org.intermine.bio.dataconversion.IdResolver
Check whether the given id is a primary identifier for this taxonId
isPrimaryIdentifier(String, String) - Method in class org.intermine.bio.dataconversion.IdResolver
Check whether the given id is a primary identifier for this taxonId
isPrimitive() - Method in class org.intermine.metadata.AttributeDescriptor
Returns true if the type of the attribute is a primitive type (rather than object).
isPrimitive() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Return true if the end element of the path is an attribute and the attribute is a primitive type.
isProfileCached(String) - Method in class org.intermine.api.profile.ProfileManager
Check if the profile, whose username is given in input, has been cached by the profile cache
isPublic(InterMineBag) - Method in class org.intermine.api.bag.BagManager
Return true if the bag is public.
isPublic() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
Returns whether this query is publicly accessible.
isRangeSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing constraint and a range has been entered.
isRedundant() - Method in class org.intermine.bio.ontology.OboRelation
 
isReference() - Method in class org.intermine.metadata.FieldDescriptor
Is this FieldDescriptor a reference?
isReference() - Method in class org.intermine.pathquery.Node
Gets the value of reference
isReference() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns true if the path represents a reference.
isRelatedTo(Constraint, FromElement) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Returns true if the constraint is associated with the given FromElement.
isRelatedToNothing(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Returns true if the given constraint is related to no FromElement.
isRequired(PathConstraint) - Method in class org.intermine.template.TemplateQuery
Returns whether a constraint is required.
isReservedWord(String) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Returns true if the given String is an IQL reserved word.
isReverseReference() - Method in class org.intermine.web.logic.query.MetadataNode
Returns true if this path is a reverse reference back onto the previous node.
isRO() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
 
isRootPath() - Method in class org.intermine.pathquery.Path
Return true if this path represents just the starting class, e.g.
isRW() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
 
isSectionOnRight() - Method in class org.intermine.web.logic.config.FieldConfig
Whether this field should be rendered in its own section on the right side of the page.
isSelectable() - Method in class org.intermine.api.results.Column
Gets the value of selectable
isSelected(String) - Method in class org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient
Return true if the correction coefficient is selected
isSelected() - Method in class org.intermine.web.logic.query.MetadataNode
Get the value of selected
isSelected() - Method in class org.intermine.web.logic.TreeNode
Is this node selected?
isSelected(String) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient
Return true if the correction coefficient is selected
isShowExtraConstraint() - Method in class org.intermine.web.logic.query.DisplayConstraint
 
isSingleBatch() - Method in class org.intermine.api.results.WebResults
Returns true if the results are known to be contained in a single batch.
isSingleBatch() - Method in interface org.intermine.api.results.WebTable
Returns true if the results are known to be contained in a single batch.
isSingleBatch() - Method in class org.intermine.objectstore.query.Results
Returns true if the results are known to fit entirely within the first batch.
isSingleBatch() - Method in class org.intermine.objectstore.query.ResultsBatches
Returns true if the results are known to fit entirely within the first batch.
isSingleton() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns true if the SELECT list is empty or if singleton results are requested.
isSizeEstimate() - Method in class org.intermine.api.results.WebResults
Check whether the result of getEstimatedSize() is an estimate
isSizeEstimate() - Method in interface org.intermine.api.results.WebTable
Check whether the result of getEstimatedSize() is an estimate
isSizeEstimate() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Check whether the result of getSize is an estimate
isStored - Variable in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder
 
ISSUE_KEYS - Static variable in class org.intermine.api.bag.BagQueryResult
keys of the map in a set
issueToken(Profile, int) - Method in class org.intermine.webservice.server.JWTBuilder
Issue a new token for the given profile.
IssueTokenTask - Class in org.intermine.web.task
A task that will issue a signed JWT token for the current configuration.
IssueTokenTask() - Constructor for class org.intermine.web.task.IssueTokenTask
 
isSummarised(ApiTemplate) - Method in class org.intermine.api.template.TemplateSummariser
Returns true if the given template has been summarised.
isSuperUser - Variable in class org.intermine.api.profile.Profile
 
isSuperuser() - Method in class org.intermine.api.profile.Profile
Return true if and only if the user logged is superuser
isSuperuser() - Method in class org.intermine.api.util.AnonProfile
 
isSuperUser(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Return true if and only if the current user if the superuser.
isThisAHuman() - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary
 
isThisAMouser() - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary
 
isToUpgrade() - Method in class org.intermine.api.profile.InterMineBag
Return true if the status bag is to_upgrade, otherwise false
isTransitive() - Method in class org.intermine.bio.ontology.OboTypeDefinition
 
isTreatColNames() - Method in class org.intermine.web.tags.table.TableTag
 
isTrue(Map<?, ?>, String) - Static method in class org.intermine.bio.ontology.OboParser
Given the tag+value map for a term, return whether it's true or false
isTruncated() - Method in class org.intermine.metadata.StringUtil.LineWrappedString
Returns whether the String had to be truncated.
isTruncated(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns true if a query using the given table-mastering ClassDescriptor would require a constraint on the className field.
isUncompressed() - Method in class org.intermine.webservice.server.WebService
 
isUniquelyMappedEnsemblId(String, String) - Method in class org.intermine.bio.dataconversion.NcbiGeneInfoParser
Return true if the given Ensembl identifier is assigned to only one gene for the taxon specified.
isUniqueSymbol(String, String) - Method in class org.intermine.bio.dataconversion.NcbiGeneInfoParser
Return true if the given symbol is is assigned to only one gene for the taxon specified.
isUpdated - Variable in class org.intermine.api.profile.PathQueryUpdate
 
isUpdated() - Method in class org.intermine.api.profile.PathQueryUpdate
Return true if the pathquery has been updated
isValid(String, String, String, UserProfile) - Method in interface org.intermine.api.profile.TagChecker
Returns true if and only the given arguments are valid fields for a tag of this type.
isValid() - Method in class org.intermine.pathquery.PathQuery
Returns true if the query verifies correctly.
isValidEditableConstraintType() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
Return true if this type of constraint can be set as editable in a template query - i.e. if it is an attribute or lookup constraint or null constraint.
isValidFastaQuery(PathQuery) - Static method in class org.intermine.bio.web.logic.SequenceFeatureExportUtil
 
isValidName(String) - Static method in class org.intermine.api.util.NameUtil
Verifies names (bags, queries, etc) only contain A-Z, a-z, 0-9, underscores and dashes.
isValidName(String, boolean) - Static method in class org.intermine.api.util.NameUtil
Verifies names (bags, queries, etc) only contain A-Z, a-z, 0-9, underscores and dashes.
isValidRange() - Method in class org.intermine.web.logic.query.DisplayConstraint
 
isValidSequenceFeatureQuery(PathQuery) - Static method in class org.intermine.bio.web.logic.SequenceFeatureExportUtil
true if valid feature
isValidTagName(String) - Static method in class org.intermine.api.profile.TagManager
TODO this should use the same validation method the other classes use Verifies that tag name can only contain A-Z, a-z, 0-9, '_', '-', ' ', ':', '.'
isValidValue(String) - Method in class org.intermine.bio.chado.config.MatchingFieldConfigAction
Validate a value for this field by matching with pattern set in the constructor.
isValueSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing constraint and an attribute value or LOOKUP constraint was selected.
isVerbose() - Method in class org.intermine.sql.precompute.QueryOptimiserContext
Returns true if the optimiser will print out stuff.
isVersionAtLeast(String) - Method in class org.intermine.sql.Database
Return true if the database version is at least as high as the test number given, taking into account major and minor versions. e.g. test if database is at least 9.2
isVisible() - Method in class org.intermine.api.results.Column
Gets the value of visible
isWindowsClient(HttpServletRequest) - Static method in class org.intermine.web.logic.RequestUtil
 
isWithinLimit(String) - Method in class org.intermine.webservice.server.core.RateLimitHistory
Check that this requester is within their limit.
isZip() - Method in class org.intermine.webservice.server.WebService
 
Item - Class in org.intermine.webservice.client.results
A representation of an individual result from the web-services.
Item(ServiceFactory, String, Map<String, Object>) - Constructor for class org.intermine.webservice.client.results.Item
Construct an Item.
Item - Class in org.intermine.xml.full
Representation of an object
Item() - Constructor for class org.intermine.xml.full.Item
Construct an item.
Item(Model, String, String, String) - Constructor for class org.intermine.xml.full.Item
Construct an item.
Item(String, String, String) - Constructor for class org.intermine.xml.full.Item
Construct an item with no Model.
ItemFactory - Class in org.intermine.xml.full
ItemFactory class
ItemFactory() - Constructor for class org.intermine.xml.full.ItemFactory
Create an ItemFactory that isn't specific to a particular model.
ItemFactory(Model) - Constructor for class org.intermine.xml.full.ItemFactory
Create an ItemFactory specific to a particular model.
ItemFactory(Model, String) - Constructor for class org.intermine.xml.full.ItemFactory
Create an ItemFactory specific to a particular model.
ItemHelper - Class in org.intermine.xml.full
Class providing Item utility methods
ItemList - Class in org.intermine.webservice.client.lists
A representation of a list of objects stored on the server.
items - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler
 
ItemToObjectTranslator - Class in org.intermine.dataconversion
Translator that translates fulldata Items to business objects
ItemToObjectTranslator(Model, ObjectStore) - Constructor for class org.intermine.dataconversion.ItemToObjectTranslator
Constructor
ItemWriter - Interface in org.intermine.dataconversion
Stores Items in something - an objectstore or otherwise.
iter - Variable in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator
 
iterateOverDependencies(String, List<String>, List) - Method in class org.intermine.task.Dependencies
Step over each dependency mentioned in depsString and record it.
iterator() - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
iterator() - Method in class org.intermine.api.results.WebResults
 
iterator() - Method in class org.intermine.api.search.SearchResults
 
iterator() - Method in class org.intermine.objectstore.proxy.ProxyCollection
iterator() - Method in class org.intermine.objectstore.query.Results
iterator() - Method in class org.intermine.util.ConsistentSet
Return an iterator for the elements in the Set.
iterator() - Method in class org.intermine.util.IteratorIterable
Returns the iterator.
iterator() - Method in class org.intermine.util.PseudoSet
iterator - Variable in class org.intermine.util.SynchronisedIterator
 
iterator() - Method in class org.intermine.webservice.client.lists.ItemList
 
iterator() - Method in class org.intermine.webservice.client.results.ResultRowList
 
iterator() - Method in class org.intermine.webservice.server.core.TableRowIterator
 
iteratorFrom(int) - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
iteratorFrom(int) - Method in class org.intermine.api.results.WebResults
 
iteratorFrom(int) - Method in class org.intermine.objectstore.query.Results
Returns an iterator over the List, starting from the given position.
IteratorIterable<T> - Class in org.intermine.util
This is an Iterable that returns a given Iterator.
IteratorIterable(Iterator<T>) - Constructor for class org.intermine.util.IteratorIterable
Constructs an Iterable from an Iterator.
iteratorIterator - Variable in class org.intermine.util.CombinedIterator
 

J

javaiseClassName(String) - Static method in class org.intermine.metadata.TypeUtil
Filter a URI fragment to remove illegal characters
javaisePackageName(String) - Static method in class org.intermine.metadata.TypeUtil
Filter a string to remove illegal characters and join the rest in lower case.
JavaModelOutput - Class in org.intermine.codegen
Maps InterMine metadata to Java source files
JavaModelOutput(Model, File) - Constructor for class org.intermine.codegen.JavaModelOutput
Constructor.
javaNameToSO(String) - Static method in class org.intermine.bio.util.BioConverterUtil
Get SO name for Java class, eg.
JBrowseDisplayer - Class in org.intermine.bio.web.displayer
Displayer for JBrowse
JBrowseDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.JBrowseDisplayer
Construct with config and the InterMineAPI.
JMOLDisplayer - Class in org.intermine.bio.web.displayer
displayer for protein structures.
JMOLDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.JMOLDisplayer
Construct with config and the InterMineAPI.
Job - Interface in org.intermine.api.idresolution
 
Job.JobStatus - Enum in org.intermine.api.idresolution
 
JobInput - Interface in org.intermine.api.idresolution
 
JobJanitor - Class in org.intermine.webservice.server.idresolution
Wake up once a minute and evict old completed jobs.
JobJanitor() - Constructor for class org.intermine.webservice.server.idresolution.JobJanitor
 
JobRemovalService - Class in org.intermine.webservice.server.idresolution
 
JobRemovalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.idresolution.JobRemovalService
 
JobResultsService - Class in org.intermine.webservice.server.idresolution
 
JobResultsService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.idresolution.JobResultsService
Construct a jobs service handler.
JobStatusService - Class in org.intermine.webservice.server.idresolution
 
JobStatusService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.idresolution.JobStatusService
Construct a handler for this request.
join(Collection<?>, String) - Static method in class org.intermine.metadata.StringUtil
Returns a String formed by the delimited results of calling toString over a collection.
join(Collection<?>, String) - Static method in class org.intermine.metadata.Util
Returns a String formed by the delimited results of calling toString over a collection.
joinType - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
JSON_FORMATS - Static variable in enum org.intermine.webservice.server.Format
The JSON formats: JSON, OBJECTS, TABLE, ROWS
JSONCountFormatter - Class in org.intermine.webservice.server.output
A formatter that presents count results as JSON.
JSONCountFormatter() - Constructor for class org.intermine.webservice.server.output.JSONCountFormatter
 
JSONDataTableRowIterator - Class in org.intermine.webservice.server.output
 
JSONDataTableRowIterator(ExportResultsIterator) - Constructor for class org.intermine.webservice.server.output.JSONDataTableRowIterator
Constructor
JSONDataTableRowResultProcessor - Class in org.intermine.webservice.server.output
A result processor for result rows.
JSONDataTableRowResultProcessor() - Constructor for class org.intermine.webservice.server.output.JSONDataTableRowResultProcessor
Constructor.
JSONFormatter - Class in org.intermine.webservice.server.output
Base class for formatters that process JSON data.
JSONFormatter() - Constructor for class org.intermine.webservice.server.output.JSONFormatter
Constructor
JSONFormattingException - Exception in org.intermine.webservice.server.output
 
JSONFormattingException(String) - Constructor for exception org.intermine.webservice.server.output.JSONFormattingException
 
JSONFormattingException(String, Throwable) - Constructor for exception org.intermine.webservice.server.output.JSONFormattingException
 
JSONFormattingException(Throwable) - Constructor for exception org.intermine.webservice.server.output.JSONFormattingException
 
JSONListFormatter - Class in org.intermine.webservice.server.lists
 
JSONListFormatter(InterMineAPI, Profile, boolean) - Constructor for class org.intermine.webservice.server.lists.JSONListFormatter
Construct a list formatter.
JSONObjectFormatter - Class in org.intermine.webservice.server.output
 
JSONObjectFormatter() - Constructor for class org.intermine.webservice.server.output.JSONObjectFormatter
Constructor
JSONObjResultProcessor - Class in org.intermine.webservice.server.output
 
JSONObjResultProcessor() - Constructor for class org.intermine.webservice.server.output.JSONObjResultProcessor
Constructor.
JSONResult - Class in org.intermine.webservice.client.results
 
JSONResult(HttpConnection) - Constructor for class org.intermine.webservice.client.results.JSONResult
Constructor
JSONResult(String) - Constructor for class org.intermine.webservice.client.results.JSONResult
Constructor with a string
JSONResultFormatter - Class in org.intermine.webservice.server.output
 
JSONResultFormatter() - Constructor for class org.intermine.webservice.server.output.JSONResultFormatter
 
JSONResultProcessor - Class in org.intermine.webservice.server.output
An class that defines the basic methods for processing JSON results.
JSONResultProcessor() - Constructor for class org.intermine.webservice.server.output.JSONResultProcessor
Constructor.
JSONResultsIterator - Class in org.intermine.webservice.server.output
A class to to produce a sequence of JSONObjects from a set of database rows.
JSONResultsIterator(ExportResultsIterator) - Constructor for class org.intermine.webservice.server.output.JSONResultsIterator
Constructor.
JsonRow - Class in org.intermine.webservice.client.results
Class representing a row of data as a list.
JsonRow(JSONArray) - Constructor for class org.intermine.webservice.client.results.JsonRow
Construct a new result row object backed by the given JSONArray.
JsonRow(String) - Constructor for class org.intermine.webservice.client.results.JsonRow
Construct a new result row object backed by the JSONArray which can be parsed from the given String.
JSONRowFormatter - Class in org.intermine.webservice.server.output
 
JSONRowFormatter() - Constructor for class org.intermine.webservice.server.output.JSONRowFormatter
Constructor
JSONRowIterator - Class in org.intermine.webservice.server.output
 
JSONRowIterator(ExportResultsIterator, InterMineAPI) - Constructor for class org.intermine.webservice.server.output.JSONRowIterator
Constructor
JsonRowMap - Class in org.intermine.webservice.client.results
Class representing a row of data as a map.
JsonRowMap(JSONArray, List<String>) - Constructor for class org.intermine.webservice.client.results.JsonRowMap
Construct a result-row with a JSONArray as its backing data store.
JsonRowMap(String, List<String>) - Constructor for class org.intermine.webservice.client.results.JsonRowMap
Construct a result-row with a String as its backing data store.
JSONRowResultProcessor - Class in org.intermine.webservice.server.output
A result processor for result rows.
JSONRowResultProcessor(InterMineAPI) - Constructor for class org.intermine.webservice.server.output.JSONRowResultProcessor
Constructor.
JSONRowResultProcessor(InterMineAPI, JSONRowResultProcessor.Verbosity) - Constructor for class org.intermine.webservice.server.output.JSONRowResultProcessor
Construct a row result processor.
JSONRowResultProcessor.Verbosity - Enum in org.intermine.webservice.server.output
 
JSONService - Class in org.intermine.webservice.server.core
A Service that has specialisations for supplying JSON.
JSONService(InterMineAPI) - Constructor for class org.intermine.webservice.server.core.JSONService
Constructor
JSONSummaryProcessor - Class in org.intermine.webservice.server.output
A processor for summary results in JSON format.
JSONSummaryProcessor() - Constructor for class org.intermine.webservice.server.output.JSONSummaryProcessor
 
JSONTableFormatter - Class in org.intermine.webservice.server.output
 
JSONTableFormatter() - Constructor for class org.intermine.webservice.server.output.JSONTableFormatter
Constructor.
JSONTableResultProcessor - Class in org.intermine.webservice.server.output
 
JSONTableResultProcessor() - Constructor for class org.intermine.webservice.server.output.JSONTableResultProcessor
Constructor.
JSONWidgetProcessor - Class in org.intermine.webservice.server.widget
 
JSStrings - Class in org.intermine.api.query.codegen
 
JWTBuilder - Class in org.intermine.webservice.server
A class that encapsulates the logic required to generate JWT tokens for users.
JWTBuilder(PrivateKey, String) - Constructor for class org.intermine.webservice.server.JWTBuilder
Constructor
JWTBuilder(JWTBuilder.Algorithm, PrivateKey, String) - Constructor for class org.intermine.webservice.server.JWTBuilder
Constructor
JWTBuilder.Algorithm - Enum in org.intermine.webservice.server
The signing algorithms this builder supports.
JWTVerifier - Class in org.intermine.webservice.server
A class to encapsulate the logic for verifying identity claims as represented as JWTs (JSON Web Tokens).
JWTVerifier(PublicKeySource, Properties) - Constructor for class org.intermine.webservice.server.JWTVerifier
Construct a verifier.
JWTVerifier.Verification - Class in org.intermine.webservice.server
The result of a successful verification.
JWTVerifier.VerificationError - Exception in org.intermine.webservice.server
An error that declares that something has gone wrong when trying to verify a JWT.
JWTVerifier.VerificationError(String) - Constructor for exception org.intermine.webservice.server.JWTVerifier.VerificationError
Initialise a new verification error with a message detailing the problem.

K

KeggOrthologuesConverter - Class in org.intermine.bio.dataconversion
Create orthologues based on KEGG pathways.
KeggOrthologuesConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.KeggOrthologuesConverter
Constructor
KeggPathwayConverter - Class in org.intermine.bio.dataconversion
DataConverter to load Kegg Pathways and link them to Genes
KeggPathwayConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.KeggPathwayConverter
Constructor
KEY_CALLBACK - Static variable in class org.intermine.webservice.server.output.JSONFormatter
The key for the callback
KEY_COLUMN_HEADERS - Static variable in class org.intermine.webservice.server.output.HTMLTableFormatter
The key for setting headers
KEY_COLUMN_HEADERS - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the title.
KEY_COUNT - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the count.
KEY_CURRENT_PAGE - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attribute for the current page
KEY_DEFINITIONS - Static variable in class org.intermine.metadata.Util
Name of the key under which to store the serialized version of the key definitions
KEY_DEFINITIONS - Static variable in class org.intermine.modelproduction.MetadataManager
Name of the key under which to store the serialized version of the key definitions
KEY_DESCRIPTION - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the description.
KEY_EXPORT_CSV_URL - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the CSV export URL.
KEY_EXPORT_TSV_URL - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the TSV export URL.
KEY_HEADER_OBJS - Static variable in class org.intermine.webservice.server.output.JSONFormatter
Things that should go into the header
KEY_INTRO - Static variable in class org.intermine.webservice.server.output.JSONFormatter
the key for the result object.
KEY_KV_PAIRS - Static variable in class org.intermine.webservice.server.output.JSONFormatter
A map of optional key value pairs that should go in the header of the object.
KEY_MODEL_NAME - Static variable in class org.intermine.webservice.server.output.JSONResultFormatter
The key for the model name
KEY_NEXT_PAGE - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the next page
KEY_OUTRO - Static variable in class org.intermine.webservice.server.output.JSONFormatter
The way to wrap up after the result.
KEY_PREVIOUS_PAGE - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the previous page
KEY_QUOTE - Static variable in class org.intermine.webservice.server.output.JSONFormatter
Whether we should quote the result item.
KEY_ROOT_CLASS - Static variable in class org.intermine.webservice.server.output.JSONResultFormatter
The key for the root class
KEY_TIME - Static variable in class org.intermine.webservice.server.output.JSONFormatter
The key for the execution time
KEY_TITLE - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the title.
KEY_VIEWS - Static variable in class org.intermine.webservice.server.output.JSONResultFormatter
The key for the views
KeyDecoder - Interface in org.intermine.web.security
Classes that can decode public keys from strings.
keyField - Variable in class org.intermine.api.results.ResultElement
 
KeyFormatException - Exception in org.intermine.api.query
 
KeyFormatException(String, NumberFormatException) - Constructor for exception org.intermine.api.query.KeyFormatException
 
KEYLESS_CLASSES_MAP - Static variable in class org.intermine.web.logic.Constants
Key for a Map from class name to Boolean.TRUE for all classes in the model that do not have any class keys.
KeySearchTrack - Class in org.intermine.api.tracker.track
 
KeySearchTrack(String, String, String, Timestamp) - Constructor for class org.intermine.api.tracker.track.KeySearchTrack
 
KeySearchTracker - Class in org.intermine.api.tracker
 
KeySearchTracker(Connection, Queue<Track>) - Constructor for class org.intermine.api.tracker.KeySearchTracker
Build a search tracker
keySet() - Method in class org.intermine.util.AlwaysMap
keySet() - Method in class org.intermine.util.IdentityMap
keySet() - Method in class org.intermine.util.ReferenceMap
KeySigner - Class in org.intermine.web.security
Issue certificates for keys we trust.
KeySigner(PrivateKey, String, int, String) - Constructor for class org.intermine.web.security.KeySigner
Build a new signer.
KeySigner.SigningException - Exception in org.intermine.web.security
Errors thrown when signing certificates.
KeySourceException - Exception in org.intermine.web.security
Errors encountered when using a PublicKeySource
KeySourceException(Throwable) - Constructor for exception org.intermine.web.security.KeySourceException
An error caused by another error
KeyStoreBuilder - Class in org.intermine.web.security
Build a key store from some options and possibly a keystore file.
KeyStoreBuilder(Properties, ResourceOpener) - Constructor for class org.intermine.web.security.KeyStoreBuilder
Construct a new KeyStoreBuilder.
KeyStorePublicKeySource - Class in org.intermine.web.security
A public key store that reads keys from a key store.
KeyStorePublicKeySource(KeyStore) - Constructor for class org.intermine.web.security.KeyStorePublicKeySource
Build a key source that reads them from a key store.
KeyStoreTask - Class in org.intermine.web.task
Base task for tasks that require a key store.
KeyStoreTask() - Constructor for class org.intermine.web.task.KeyStoreTask
 
KeywordSearch - Class in org.intermine.api.lucene
Allows for full-text searches over all metadata using the apache lucene engine.
KeywordSearchFacet - Class in org.intermine.api.lucene
container for one faceting field, the current faceting value and the list of possible items
KeywordSearchFacet(String, String, String, List<BrowseFacet>) - Constructor for class org.intermine.api.lucene.KeywordSearchFacet
constructor
KeywordSearchFacetData - Class in org.intermine.api.lucene
container class for a facet field and its settings
KeywordSearchFacetData(String, String, KeywordSearchFacetType) - Constructor for class org.intermine.api.lucene.KeywordSearchFacetData
convenience constructor for single field
KeywordSearchFacetData(String[], String, KeywordSearchFacetType) - Constructor for class org.intermine.api.lucene.KeywordSearchFacetData
constructor
KeywordSearchFacetType - Enum in org.intermine.api.lucene
type of faceting to use see http://snaprojects.jira.com/wiki/display/BOBO/Create+a+Browse+Index
KeywordSearchHit - Class in org.intermine.api.lucene
container class to hold a document found in an keyword search together with its object and score
KeywordSearchHit(float, Document, InterMineObject) - Constructor for class org.intermine.api.lucene.KeywordSearchHit
constructor
KeywordSearchResult - Class in org.intermine.web.search
Container for a single result row from the keyword search
KeywordSearchResult(WebConfig, InterMineObject, Map<String, List<FieldDescriptor>>, ClassDescriptor, float, Map<String, TemplateQuery>, String) - Constructor for class org.intermine.web.search.KeywordSearchResult
create the container object - automatically reads fields and saves the results in members
KeywordSearchResultsController - Class in org.intermine.web.struts
Controller for keyword search.
KeywordSearchResultsController() - Constructor for class org.intermine.web.struts.KeywordSearchResultsController
 

L

LabelsSummaryAction - Class in org.intermine.web.struts
An action that presents how all the labels configured for classes and their top-level fields appear.
LabelsSummaryAction() - Constructor for class org.intermine.web.struts.LabelsSummaryAction
 
labourer - Variable in class org.intermine.webservice.server.output.FlatFileFormatter
 
last(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction
Change to the last results page
last(int) - Method in class org.intermine.webservice.client.results.Page
Get the last page.
lastBatch - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
lastGet - Variable in class org.intermine.objectstore.query.Results
 
lastIndexOf(Object) - Method in class org.intermine.webservice.client.results.ResultRowList
 
lastPage() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Go to the last page
lastSource - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
lastTickle - Variable in class org.intermine.web.logic.query.QueryMonitorTimeout
Time of last call to tickle.
LAYOUT_PARAMETER - Static variable in class org.intermine.webservice.server.query.result.QueryResultRequestParser
Layout parameter name.
Lazy - Interface in org.intermine.objectstore.proxy
Class which uses an ObjectStore to perform lazy fetching of data
LazyCollection<E> - Interface in org.intermine.objectstore.proxy
Class which uses an ObjectStore to perform lazy fetching of data
lazyList() - Method in class org.intermine.webservice.server.core.JSONService
 
lazyList() - Method in class org.intermine.webservice.server.data.DataService
 
lcm(int, int) - Static method in class org.intermine.metadata.Util
Takes two integers, and returns the lowest common multiple.
LEAF_DESCRIPTORS_MAP - Static variable in class org.intermine.web.logic.Constants
Servlet attribute.
LEAST - Static variable in class org.intermine.objectstore.query.QueryExpression
Return the lowest value from two expressions, e.g.
LEAST - Static variable in class org.intermine.sql.query.Function
LEAST(x, y) - takes two operands
left - Variable in class org.intermine.objectstore.query.OverlapConstraint
 
left - Variable in class org.intermine.sql.query.Constraint
 
left - Variable in class org.intermine.sql.query.InListConstraint
 
left - Variable in class org.intermine.sql.query.SubQueryConstraint
 
LEFT_BRACE - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
LEFT_FALSE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints, where the left is always false.
LEFT_FALSE_RIGHT_TRUE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints, where the left is always false, and the right is always true.
LEFT_TRUE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints, where the left is always true.
LEFT_TRUE_RIGHT_FALSE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints, where the left is always true, and the right is always false.
length() - Method in class org.intermine.model.StringConstructor
length - Variable in class org.intermine.objectstore.query.ClobAccess
 
length() - Method in class org.intermine.objectstore.query.ClobAccess
Returns the length of this character sequence.
length() - Method in class org.intermine.objectstore.query.PendingClob
Returns the length of this character sequence.
LESS - Static variable in class org.intermine.sql.query.AbstractValue
Describes one AbstractValue as being less than another AbstractValue.
LESS_THAN - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is less than the second
LESS_THAN_EQUALS - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is less than or equal to the second
lessOrEqual(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
Compare the value of this AbstractValue with another to see if it is less or equal.
lessThan(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be less than a value.
lessThan(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
Compare the value of this AbstractValue with another to see if it is less.
lessThanEqualTo(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be less than or equal to a value.
LiftOverService - Class in org.intermine.bio.web.logic
Communication between intermine and liftover server in a way as posting http request from the webapp, avoiding cross-domian issue.
LiftOverService() - Constructor for class org.intermine.bio.web.logic.LiftOverService
 
like(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be LIKE a value.
LIKE - Static variable in class org.intermine.sql.query.Constraint
An operation for this constraint indicating that left should be pattern-matched against right.
limit - Variable in class org.intermine.sql.query.Query
 
LIMIT_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Name of size parameter that determines number of returned results.
limitedContext - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
LimitedMap<K,V> - Class in org.intermine.api.util
A caching map that drops its eldest entries if the map grows beyond a certain size.
LimitedMap(int) - Constructor for class org.intermine.api.util.LimitedMap
 
LimitOffsetQuery - Class in org.intermine.sql.precompute
A class specifically for use with the OptimiserCache, designed to split a SQL string into its functional part, and the limit and offset.
LimitOffsetQuery(String) - Constructor for class org.intermine.sql.precompute.LimitOffsetQuery
Creates a new LimitOffsetQuery object from this query string.
linkedHashMapAdd(LinkedHashMap<K, V>, K, K, V) - Static method in class org.intermine.util.CollectionUtil
Return a copy of the given map with the object inserted at the given index.
linkFile - Variable in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask
 
LinkGeneratorBase - Class in org.intermine.webservice.server
Base class for link generators.
LinkGeneratorBase() - Constructor for class org.intermine.webservice.server.LinkGeneratorBase
Empty constructor.
LinkRedirectManager - Class in org.intermine.api
Class to manage external links.
LinkRedirectManager(Properties) - Constructor for class org.intermine.api.LinkRedirectManager
Constructor
linkRedirector - Variable in class org.intermine.api.InterMineAPI
 
list(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoadQueryAction
Load a query using given list
list(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoadTemplateAction
Load a template from template name passed as parameter.
LIST_NAME_KEY - Static variable in class org.intermine.webservice.server.lists.AbstractListService
 
LIST_SEPARATOR - Static variable in class org.intermine.webservice.server.lists.ListInput
The separator used between lists when passed joined together.
LIST_SIZE_KEY - Static variable in class org.intermine.webservice.server.lists.AbstractListService
 
LIST_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of class that tracks lists
LIST_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of table that tracks lists
ListAppendService - Class in org.intermine.webservice.server.lists
 
ListAppendService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListAppendService
 
ListBuildMode - Enum in org.intermine.api.tracker.util
 
ListCreationInput - Class in org.intermine.webservice.server.lists
Class representing the input to a list creation request.
ListCreationInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.ListCreationInput
Constructor.
ListDeletionService - Class in org.intermine.webservice.server.lists
A service for deleting lists from the user-profile database.
ListDeletionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListDeletionService
Constructor.
ListDifferenceService - Class in org.intermine.webservice.server.lists
A service for performing a symmetric difference operation on a collection of lists.
ListDifferenceService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListDifferenceService
Constructor
ListFormatter - Interface in org.intermine.webservice.server.lists
The common interface for formatters that know how to format lists.
ListFunctions - Class in org.intermine.webservice.server.core
Similar to Apache CollectionUtils - but with Generics.
ListInput - Class in org.intermine.webservice.server.lists
Class representing input to a list service request.
ListInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.ListInput
Parse the values from the request, and validate them.
ListIntersectionService - Class in org.intermine.webservice.server.lists
A service that intersects one or more lists.
ListIntersectionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListIntersectionService
 
listIterator() - Method in class org.intermine.webservice.client.results.ResultRowList
 
listIterator(int) - Method in class org.intermine.webservice.client.results.ResultRowList
 
listLeft - Variable in class org.intermine.web.struts.ModifyBagForm
 
ListMaker<T> - Interface in org.intermine.webservice.server.lists
The type of things that can make lists.
ListMakerService - Class in org.intermine.webservice.server.lists
A base class for all list services that create lists.
ListMakerService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListMakerService
Constructor.
ListManager - Class in org.intermine.webservice.server.core
Manager of public lists used by web service.
ListManager(InterMineAPI, Profile) - Constructor for class org.intermine.webservice.server.core.ListManager
ListManager constructor.
ListOperationService - Class in org.intermine.webservice.server.lists
A base class for services that perform operations on lists.
ListOperationService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListOperationService
Constructor.
listRelatedConstraints(Query, FromElement) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Return a List of Constraint objects that relate to the given FromElement.
ListRenameInput - Class in org.intermine.webservice.server.lists
Class for encapsulating the input to a list rename request.
ListRenameInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.ListRenameInput
Constructor.
ListRenameService - Class in org.intermine.webservice.server.lists
A service for renaming lists.
ListRenameService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListRenameService
Constructor.
ListRenameServlet - Class in org.intermine.webservice.server.lists
 
ListRenameServlet() - Constructor for class org.intermine.webservice.server.lists.ListRenameServlet
 
listRight - Variable in class org.intermine.web.struts.ModifyBagForm
 
Lists - Class in org.intermine.webservice.client.lists
Utilities for parsing lists from their JSON representation.
LISTS_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
The lists to operate on
listsButton - Variable in class org.intermine.web.struts.ModifyBagForm
 
ListService - Class in org.intermine.webservice.client.services
An interface to all the resources that represent list information and list operations available at an InterMine implementation.
ListService(String, String) - Constructor for class org.intermine.webservice.client.services.ListService
Use ServiceFactory instead of constructor for creating this service .
ListService.ListCreationInfo - Class in org.intermine.webservice.client.services
An abstraction of the combination of options that can be specified to generate a new list in a list creation operation.
ListService.ListCreationInfo(String) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo
Create a new options bundle with all possible optional values set to their defaults.
ListService.ListCreationInfo(PathQuery) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo
Create a new options bundle, specifying the query to use to find objects with.
ListService.ListCreationInfo(PathQuery, String) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo
Create a new options bundle, specifying the name.
ListService.ListCreationInfo(String, String) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo
Create a new options bundle, with the name taken from the supplied value.
ListService.ListCreationInfo(PathQuery, String, String) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo
Create a new options bundle, specifying the name and the description.
ListService.ListCreationInfo(String, String, String) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo
Create a new options bundle, with the name and description taken from the supplied value.
ListService.ListCreationInfo(PathQuery, String, String, Collection<? extends String>) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo
Create a new options bundle, specifying all parameters.
ListService.ListCreationInfo(String, String, String, Collection<? extends String>) - Constructor for class org.intermine.webservice.client.services.ListService.ListCreationInfo
Create a new options bundle, specifying all parameters.
ListService.ListOperationInfo - Class in org.intermine.webservice.client.services
An abstraction of the combination of options that can be specified to generate a new list in a list operation.
ListService.ListOperationInfo() - Constructor for class org.intermine.webservice.client.services.ListService.ListOperationInfo
Create a new options bundle with all values set to their defaults.
ListService.ListOperationInfo(String) - Constructor for class org.intermine.webservice.client.services.ListService.ListOperationInfo
Create a new options bundle, with all elements set to their default apart from the name, which is given.
ListService.ListOperationInfo(String, String) - Constructor for class org.intermine.webservice.client.services.ListService.ListOperationInfo
Create a new options bundle, with all elements set to their default apart from the name and the description, which are given.
ListService.ListOperationInfo(String, String, Collection<? extends String>) - Constructor for class org.intermine.webservice.client.services.ListService.ListOperationInfo
Create a new options bundle, specifying all options.
ListServiceUtils - Class in org.intermine.webservice.server.lists
Utility functions for dealing with list requests.
ListShareCreationService - Class in org.intermine.webservice.server.lists
 
ListShareCreationService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListShareCreationService
 
ListShareDeletionService - Class in org.intermine.webservice.server.lists
 
ListShareDeletionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListShareDeletionService
 
ListShareDetailsService - Class in org.intermine.webservice.server.lists
 
ListShareDetailsService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListShareDetailsService
 
ListShareServlet - Class in org.intermine.webservice.server.lists
 
ListShareServlet() - Constructor for class org.intermine.webservice.server.lists.ListShareServlet
 
ListSharingInvitationAcceptanceService - Class in org.intermine.webservice.server.lists
 
ListSharingInvitationAcceptanceService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListSharingInvitationAcceptanceService
 
ListSharingInvitationDeletionService - Class in org.intermine.webservice.server.lists
 
ListSharingInvitationDeletionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListSharingInvitationDeletionService
Construct a service handler.
ListSharingInvitationDetailsService - Class in org.intermine.webservice.server.lists
 
ListSharingInvitationDetailsService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListSharingInvitationDetailsService
 
ListSharingInvitationService - Class in org.intermine.webservice.server.lists
Invite a user to share a list.
ListSharingInvitationService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListSharingInvitationService
 
ListSharingInvitationServlet - Class in org.intermine.webservice.server.lists
 
ListSharingInvitationServlet() - Constructor for class org.intermine.webservice.server.lists.ListSharingInvitationServlet
 
ListsRequestParser - Class in org.intermine.webservice.server.lists
Request processor for ListsService that process request, validates it and returns parsed input as a parameter object.
ListsRequestParser(HttpServletRequest) - Constructor for class org.intermine.webservice.server.lists.ListsRequestParser
ListsRequestProcessor constructor.
ListsService - Class in org.intermine.webservice.server.lists
Web service that returns all public lists (bags) that contain object with specified id.
ListsService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListsService
Constructor
ListsServiceInput - Class in org.intermine.webservice.server.lists
ListsServiceInput is parameter object representing parameters for ListService web service.
ListsServiceInput() - Constructor for class org.intermine.webservice.server.lists.ListsServiceInput
 
ListSubtractionService - Class in org.intermine.webservice.server.lists
A service for subtracting one group of lists from another group of lists to produce a new list.
ListSubtractionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListSubtractionService
Constructor
ListTagAddingService - Class in org.intermine.webservice.server.lists
A service for adding tags to a list.
ListTagAddingService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListTagAddingService
Constructor.
ListTagRemovalService - Class in org.intermine.webservice.server.lists
A service for removing tags from a list.
ListTagRemovalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListTagRemovalService
Constructor.
ListTagService - Class in org.intermine.webservice.server.lists
A service for getting the tags of a list.
ListTagService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListTagService
Constructor.
ListTrack - Class in org.intermine.api.tracker.track
Class to represent the track for the lists objects.
ListTrack(String, int, ListBuildMode, ListTrackerEvent, String, String, Timestamp) - Constructor for class org.intermine.api.tracker.track.ListTrack
 
ListTrack(String, int, ListBuildMode, ListTrackerEvent) - Constructor for class org.intermine.api.tracker.track.ListTrack
 
LISTTRACK - Static variable in class org.intermine.api.tracker.xml.ListTrackBinding
label for XML
ListTrackBinding - Class in org.intermine.api.tracker.xml
 
ListTracker - Class in org.intermine.api.tracker
 
ListTracker(Connection, Queue<Track>) - Constructor for class org.intermine.api.tracker.ListTracker
Build a list tracker
ListTrackerEvent - Enum in org.intermine.api.tracker.util
 
LISTTRACKS - Static variable in class org.intermine.api.tracker.xml.ListTrackBinding
label for XML
ListUnionService - Class in org.intermine.webservice.server.lists
A class for exposing creating unions of lists as a resource.
ListUnionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListUnionService
Constructor.
ListUploadService - Class in org.intermine.webservice.server.lists
A class to create a new list with via a set of identifiers uploaded by a user.
ListUploadService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListUploadService
Constructor
load(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryChangeAction
Load a query.
LoadBagValuesTask - Class in org.intermine.web.task
Task to load bagvalues table in the userprofile database.
LoadBagValuesTask() - Constructor for class org.intermine.web.task.LoadBagValuesTask
 
loadClassKeyDefinitions() - Static method in class org.intermine.modelproduction.MetadataManager
Load the class key / key field definitions.
LoadDefaultTemplatesTask - Class in org.intermine.web.task
Load template queries form an XML file into a given user profile.
LoadDefaultTemplatesTask() - Constructor for class org.intermine.web.task.LoadDefaultTemplatesTask
 
loadHelpers(Properties) - Static method in class org.intermine.api.query.MainHelper
 
loadHelpers(Properties) - Static method in class org.intermine.api.query.MainHelper.RangeConfig
 
LOADING - Static variable in class org.intermine.objectstore.query.PrefetchManager
 
loadKeyDefinitions(String) - Static method in class org.intermine.metadata.Util
Load the key definitions file for the named model from the classpath
loadKeyDefinitions(String) - Static method in class org.intermine.modelproduction.MetadataManager
Load the key definitions file for the named model from the classpath
loadModel(String) - Static method in class org.intermine.metadata.ModelFactory
Load a named model from the classpath
loadProjectProperties(File) - Static method in class org.intermine.task.Dependencies
Load project properties for given project.
loadProperties(String) - Static method in class org.intermine.metadata.Util
Load a specified properties file
loadProperties(String) - Static method in class org.intermine.util.PropertiesUtil
Load a specified properties file
loadQuery(PathQuery, HttpSession, HttpServletResponse) - Static method in class org.intermine.web.logic.session.SessionMethods
Load a query into the session, cloning to avoid modifying the original
LoadQueryAction - Class in org.intermine.web.struts
Implementation of Action that sets the current Query for the session from some random XML the user has passed in, and maybe executes it.
LoadQueryAction() - Constructor for class org.intermine.web.struts.LoadQueryAction
 
LoadTemplateAction - Class in org.intermine.web.struts
Implementation of Action that runs a template
LoadTemplateAction() - Constructor for class org.intermine.web.struts.LoadTemplateAction
 
LocalMine - Class in org.intermine.api.mines
A mine that refers to the local application instance.
LocalMine(InterMineAPI, Properties) - Constructor for class org.intermine.api.mines.LocalMine
Construct a mine that refers to the local application instance.
lock - Static variable in class org.intermine.sql.logging.QueryLogger
 
locusTag - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord
 
LOG - Static variable in class org.intermine.api.bag.operations.BagOperation
 
LOG - Static variable in class org.intermine.api.profile.InterMineBag
 
LOG - Static variable in class org.intermine.api.profile.InvalidBag
 
LOG - Static variable in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
 
LOG - Static variable in class org.intermine.api.results.WebResults
 
LOG - Static variable in class org.intermine.bio.dataconversion.ChadoDBConverter
 
LOG - Static variable in class org.intermine.bio.dataconversion.EnsemblIdResolverFactory
 
LOG - Static variable in class org.intermine.bio.dataconversion.EntrezOrganismRetriever
 
LOG - Static variable in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
 
LOG - Static variable in class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory
 
LOG - Static variable in class org.intermine.bio.dataconversion.HgncIdResolverFactory
 
LOG - Static variable in class org.intermine.bio.dataconversion.HumanIdResolverFactory
 
LOG - Static variable in class org.intermine.bio.dataconversion.IdResolverService
 
LOG - Static variable in class org.intermine.bio.dataconversion.InterproGoConverter
 
LOG - Static variable in class org.intermine.bio.dataconversion.KeggOrthologuesConverter
 
LOG - Static variable in class org.intermine.bio.dataconversion.KeggPathwayConverter
 
LOG - Static variable in class org.intermine.bio.dataconversion.MgiIdentifiersResolverFactory
 
LOG - Static variable in class org.intermine.bio.dataconversion.NcbiGeneInfoParser
 
LOG - Static variable in class org.intermine.bio.dataconversion.NcbiGffGFF3SeqHandler
 
LOG - Static variable in class org.intermine.bio.dataconversion.OntologyIdResolverFactory
 
LOG - Static variable in class org.intermine.bio.dataconversion.PubMedGeneConverter
 
LOG - Static variable in class org.intermine.bio.dataconversion.RgdIdentifiersResolverFactory
 
LOG - Static variable in class org.intermine.bio.dataconversion.WormBaseIdResolverFactory
 
LOG - Static variable in class org.intermine.bio.dataconversion.ZfinIdentifiersResolverFactory
 
LOG - Static variable in class org.intermine.bio.task.GFF3ConverterTask
 
LOG - Static variable in class org.intermine.bio.util.BioUtil
 
LOG - Static variable in class org.intermine.bio.web.AttributeLinksController
 
LOG - Static variable in class org.intermine.bio.web.BioLinkRedirectManager
 
LOG - Static variable in class org.intermine.bio.web.displayer.CuratedProteinsDisplayer
 
LOG - Static variable in class org.intermine.bio.web.displayer.DiseaseDisplayer
 
LOG - Static variable in class org.intermine.bio.web.displayer.EsynDisplayer
 
LOG - Static variable in class org.intermine.bio.web.displayer.GeneIdentifiersDisplayer
 
LOG - Static variable in class org.intermine.bio.web.displayer.HomologueDisplayer
 
LOG - Static variable in class org.intermine.bio.web.displayer.JMOLDisplayer
 
LOG - Static variable in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer
 
LOG - Static variable in class org.intermine.bio.web.displayer.MinePathwaysDisplayer
 
LOG - Static variable in class org.intermine.bio.web.displayer.MouseAllelesDisplayer
 
LOG - Static variable in class org.intermine.bio.web.displayer.OverlappingFeaturesDisplayer
 
LOG - Static variable in class org.intermine.bio.web.displayer.PublicationAnnotationsDisplayer
 
LOG - Static variable in class org.intermine.bio.web.displayer.PublicationCountsDisplayer
 
LOG - Static variable in class org.intermine.bio.web.displayer.RegulatoryRegionsDisplayer
 
LOG - Static variable in class org.intermine.bio.web.displayer.SnpToGeneDisplayer
 
LOG - Static variable in class org.intermine.bio.web.displayer.UniProtCommentsDisplayer
 
LOG - Static variable in class org.intermine.bio.web.export.ResidueFieldExporter
 
LOG - Static variable in class org.intermine.bio.web.export.SequenceHttpExporter
 
LOG - Static variable in class org.intermine.bio.web.model.GeneModel
 
LOG - Static variable in class org.intermine.bio.web.model.GeneModelCache
 
LOG - Static variable in class org.intermine.dwr.AjaxServices
 
LOG - Static variable in class org.intermine.dwr.TrackAjaxServices
 
LOG - Static variable in class org.intermine.model.testmodel.web.RedirectManager
 
log - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
LOG - Static variable in class org.intermine.pathquery.Path
 
log(Query, Writer) - Static method in class org.intermine.sql.logging.QueryLogger
Allows a Query to be logged
LOG - Static variable in class org.intermine.task.DynamicAttributeTask
 
LOG - Static variable in class org.intermine.task.FileConverterTask
 
LOG - Static variable in class org.intermine.web.displayer.DisplayerManager
 
LOG - Static variable in class org.intermine.web.logic.export.http.StandardHttpExporter
 
LOG - Static variable in class org.intermine.web.logic.export.ResultElementConverter
 
LOG - Static variable in class org.intermine.web.logic.results.DisplayField
 
LOG - Static variable in class org.intermine.web.logic.results.InlineResultsTable
 
LOG - Static variable in class org.intermine.web.logic.session.SessionMethods
 
LOG - Static variable in class org.intermine.web.logic.WebUtil
 
LOG - Static variable in class org.intermine.web.struts.ContactAction
 
LOG - Static variable in class org.intermine.web.struts.CreateTemplateAction
 
LOG - Static variable in class org.intermine.web.struts.ExportQueryAction
 
LOG - Static variable in class org.intermine.web.struts.HtmlHeadController
 
LOG - Static variable in class org.intermine.web.struts.InterMineExceptionHandler
 
LOG - Static variable in class org.intermine.web.struts.ObjectTrailController
 
LOG - Static variable in class org.intermine.web.struts.ObjectViewController
 
LOG - Static variable in class org.intermine.web.struts.PollQueryAction
 
LOG - Static variable in class org.intermine.web.struts.QueryBuilderChange
 
LOG - Static variable in class org.intermine.web.struts.QueryBuilderController
 
LOG - Static variable in class org.intermine.web.struts.RequestPasswordAction
 
LOG - Static variable in class org.intermine.web.struts.SaveBagAction
 
LOG - Static variable in class org.intermine.web.struts.SaveFromIdsToBagAction
 
LOG - Static variable in class org.intermine.web.struts.SaveQueryAction
 
LOG - Static variable in class org.intermine.web.struts.SummariseTemplatesAction
 
LOG - Static variable in class org.intermine.web.struts.TableExportAction
 
LOG - Static variable in class org.intermine.web.struts.TemplatesExportAction
 
LOG - Static variable in class org.intermine.web.struts.WebserviceCodeGenAction
 
LOG - Static variable in class org.intermine.webservice.server.query.CodeService
 
logBeforeExecute - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
logError(String) - Method in class org.intermine.web.task.KeyStoreTask
Log a message to standard error.
logEverything - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
logExampleQueryUse(HttpSession, String) - Static method in class org.intermine.web.logic.session.SessionMethods
Log load of an example query.
logExplains - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
LogicExpression - Class in org.intermine.pathquery
In memory representation of constraint logic expression.
LogicExpression(String) - Constructor for class org.intermine.pathquery.LogicExpression
Create a new instance of LogicExpression parsing the given expression.
LogicExpression.And - Class in org.intermine.pathquery
An AND operator node.
LogicExpression.Node - Class in org.intermine.pathquery
Node of parse tree.
LogicExpression.Node() - Constructor for class org.intermine.pathquery.LogicExpression.Node
 
LogicExpression.Operator - Class in org.intermine.pathquery
An operator node.
LogicExpression.Or - Class in org.intermine.pathquery
An OR operator node.
LogicExpression.Variable - Class in org.intermine.pathquery
A variable node.
LOGIN_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of class that tracks lists
LOGIN_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of table that tracks logins
LoginAction - Class in org.intermine.web.struts
Action to handle button presses on the main tile
LoginAction() - Constructor for class org.intermine.web.struts.LoginAction
 
LoginController - Class in org.intermine.web.struts
Controller for the login page.
LoginController() - Constructor for class org.intermine.web.struts.LoginController
 
LoginForm - Class in org.intermine.web.struts
The main form, using for editing constraints
LoginForm() - Constructor for class org.intermine.web.struts.LoginForm
 
LoginHandler - Class in org.intermine.web.logic.profile
 
LoginHandler() - Constructor for class org.intermine.web.logic.profile.LoginHandler
 
LoginTrack - Class in org.intermine.api.tracker.track
 
LoginTrack(String, Timestamp) - Constructor for class org.intermine.api.tracker.track.LoginTrack
 
LOGINTRACK - Static variable in class org.intermine.api.tracker.xml.LoginTrackBinding
label for XML
LoginTrackBinding - Class in org.intermine.api.tracker.xml
 
LoginTracker - Class in org.intermine.api.tracker
Class for tracking when the users log into their accounts.
LoginTracker(Connection, Queue<Track>) - Constructor for class org.intermine.api.tracker.LoginTracker
Build a login tracker
LOGINTRACKS - Static variable in class org.intermine.api.tracker.xml.LoginTrackBinding
label for XML
logMessage(String) - Method in class org.intermine.web.task.KeyStoreTask
Log a message to standard out.
LogoutAction - Class in org.intermine.web.struts
Action that invalidates the user session effectively logging the user out of intermine.
LogoutAction() - Constructor for class org.intermine.web.struts.LogoutAction
 
logQuery(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Before running a query via web services, add to query history and add a track
logTableBatch - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
logTableConnection - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
logTableName - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
logTemplateQueryUse(HttpSession, String, String) - Static method in class org.intermine.web.logic.session.SessionMethods
Log use of a template query.
LOOKUP - Static variable in class org.intermine.metadata.ConstraintOp
Special operation indicating a bag upload step should be used, for the webapp only.
lookup(String, String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path with the LOOKUP operator.
lookup(String, int) - Method in class org.intermine.sql.precompute.OptimiserCache
Attempts to find a match in the cache for an original query.
LOOKUP_CONSTRAINT - Static variable in class org.intermine.api.config.Constants
LOOKUP constraint
LOOKUP_MSG - Static variable in class org.intermine.web.logic.Constants
Session attribute that holds message when a lookup constraint has been used
lookupCategory(String) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Returns a Map from original SQL to PrecomputedTable for a given category in the manager.
lookupOs - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher
 
lookupSql(String, String) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Returns a PrecomputedTable object if one exists in the manager with the given category and original SQL string.
lookupSql(String) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Returns a PrecomputedTable object if one exists in the manager with the given original SQL string.
LookupTokeniser - Class in org.intermine.api.query
Class for tokenising identifier input.
LOOP_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
LOOP_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
 
loopQueryOp - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
loopQueryValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
LOWER - Static variable in class org.intermine.objectstore.query.QueryExpression
Lower case version of the given string
LOWER - Static variable in class org.intermine.sql.query.Function
LOWER operator - takes one operand
LT - Static variable in class org.intermine.sql.query.Constraint
An operation for this constraint indicating that left is less than right.
LuceneIndex - Class in org.intermine.web.autocompletion
Creates the indexes for LuceneObjectClasses
LuceneIndex(String) - Constructor for class org.intermine.web.autocompletion.LuceneIndex
Constructor
LuceneObjectClass - Class in org.intermine.web.autocompletion
LuceneObjectClass contains data for the autocompletion
LuceneObjectClass(String) - Constructor for class org.intermine.web.autocompletion.LuceneObjectClass
Constructor
LuceneSearchEngine - Class in org.intermine.web.autocompletion
LuceneSearchEngine for the autocompleter
LuceneSearchEngine(String) - Constructor for class org.intermine.web.autocompletion.LuceneSearchEngine
LuceneSearchEngine constructor put the indexes to memory and creates an keyword analyser
LuceneSearchEngine(RAMDirectory) - Constructor for class org.intermine.web.autocompletion.LuceneSearchEngine
LuceneSearchEngine constructor put the indexes to memory and creates an keyword analyser

M

M_N_RELATION - Static variable in class org.intermine.metadata.FieldDescriptor
A M:N relationship.
MailAction - Interface in org.intermine.web.context
The type of objects that can send themselves with an Emailer.
MailDaemon - Class in org.intermine.web.context
An runnable that will send emails delivered over a concurrent queue.
MailDaemon(ArrayBlockingQueue<MailAction>, Emailer) - Constructor for class org.intermine.web.context.MailDaemon
Create a MailDaemon
mailinglist - Variable in class org.intermine.web.struts.CreateAccountForm
 
MailUtils - Class in org.intermine.util
Mail utilities for the webapp.
main(String[]) - Static method in class org.intermine.sql.query.Query
A testing method - converts the argument into a Query object, and then converts it back to a String again.
main(String[]) - Static method in class org.intermine.web.commandline.PerformanceTester
.
MAIN - Static variable in class org.intermine.web.logic.config.HeaderConfigTitle
The first part of a page title.
MainHelper - Class in org.intermine.api.query
Helper methods for main controller and main action
MainHelper.RangeConfig - Class in org.intermine.api.query
 
MainHelper.SummaryConfig - Class in org.intermine.api.query
Controls access to configuration information on which fields should be summarised as a count of occurrences.
make(SequenceFeature) - Static method in class org.intermine.bio.web.biojava.BioSequenceFactory
Create a new BioSequence from a SequenceFeature
make(Protein) - Static method in class org.intermine.bio.web.biojava.BioSequenceFactory
Create a new BioSequence from a Protein
make(BioEntity, BioSequenceFactory.SequenceType) - Static method in class org.intermine.bio.web.biojava.BioSequenceFactory
Create a new BioSequence from a BioEntity, given its SequenceType
makeAnatomyTerm(String) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
phenotype annotation creates and stores anatomy terms.
makeAnatomyTerm(String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
 
makeBEDRecord(SequenceFeature) - Static method in class org.intermine.bio.web.export.BEDUtil
Create a BEDRecord from a LocatedSequenceFeature.
makeBEDRecord(SequenceFeature, boolean) - Static method in class org.intermine.bio.web.export.BEDUtil
Create a BEDRecord from a LocatedSequenceFeature.
makeFeature(Integer, String, String, String, String, int, int) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Make a new feature
makeFeature(Integer, String, String, String, String, int, int) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
copied from FlyBaseProcessor Make a new feature
makeFeature(Integer, String, String, String, String, int, int) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Make a new feature
makeFeatureData(int, String, String, String, String, int, int) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Create and store a new Item, returning a FeatureData object for the feature.
makeFeatureData(int, String, String, String, String, int, int) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Create and store a new Item, returning a FeatureData object for the feature.
makeForward(ActionMapping, HttpServletRequest, PagedTable) - Method in class org.intermine.web.struts.ChangeTableAction
Create a forward with parameters setting start item and page size.
makeGAFRecord(SequenceFeature) - Static method in class org.intermine.bio.web.export.GAFUtil
Create a GAFRecord from a LocatedSequenceFeature.
makeGFF3Record(SequenceFeature, Map<String, String>, String, Map<String, List<String>>) - Static method in class org.intermine.bio.web.export.GFF3Util
Create a GFF3Record from a SequenceFeature.
makeGFF3Record(SequenceFeature, Map<String, String>, String, Map<String, List<String>>, boolean) - Static method in class org.intermine.bio.web.export.GFF3Util
Create a GFF3Record from a SequenceFeature.
makeInteractionExperiment(String, String) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Return the item identifier of the Interaction Item for the given pubmed id, creating the Item if necessary.
makeItem() - Method in class org.intermine.xml.full.ItemFactory
Make an empty Item with a unique identifier.
makeItem(String) - Method in class org.intermine.xml.full.ItemFactory
Make an empty Item with the given identifier.
makeItem(String, String, String) - Method in class org.intermine.xml.full.ItemFactory
Construct an item from an identifier, a class name and the names of implemented classes
makeItem(FastPathObject) - Method in class org.intermine.xml.full.ItemFactory
Convert an Object to Item format.
makeItemForClass(String) - Method in class org.intermine.xml.full.ItemFactory
Construct an item from a class name.
makeItemImpl(FastPathObject, Set<String>) - Method in class org.intermine.xml.full.ItemFactory
Convert an Object to Item format, writing the fields provided in includeFields.
makeJSONOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.jbrowse.Config
 
makeJSONOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.jbrowse.Names
 
makeJSONOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.query.result.QueryResultService
 
makeJSONOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.WebService
Make the default JSON output given the HttpResponse's PrintWriter.
makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.bio.webservice.AbstractRegionExportService
 
makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.bio.webservice.GenomicRegionSearchService
 
makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.webservice.server.lists.ListAppendService
 
makeList(T, String, Profile, Set<String>) - Method in interface org.intermine.webservice.server.lists.ListMaker
Make the list requested by the user.
makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.webservice.server.lists.ListMakerService
Make the list requested by the user.
makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.webservice.server.lists.ListOperationService
 
makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.webservice.server.lists.ListUploadService
 
makeLocation(String, String, int, int, int, int) - Method in class org.intermine.bio.dataconversion.BioDBConverter
Make a Location Relation between a LocatedSequenceFeature and a Chromosome.
makeLocation(String, String, String, String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioFileConverter
Make a Location between a Feature and a Chromosome.
makeLocation(int, int, int, FeatureData, FeatureData, int, int) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
note: featureId is needed only by modMine Make a Location between a SequenceFeature and a Chromosome.
makeLocation(int, int, int, FeatureData, FeatureData, int, int) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Make a Location between a SequenceFeature and a Chromosome.
makeLocation(int, int, int, FeatureData, FeatureData, int, int) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Make a Location between a SequenceFeature and a Chromosome.
makeMultiTypeConstraint(Model, QueryNode, PathConstraintMultitype) - Static method in class org.intermine.api.query.MainHelper
Construct a new multi-type constraint.
makeNodes(String, Model, boolean, PathQuery, WebConfig, Map<String, List<FieldDescriptor>>, BagManager, Profile, ObjectStoreSummary) - Static method in class org.intermine.web.logic.querybuilder.ModelBrowserHelper
Given a path, render a set of metadata Nodes to the relevant depth
makeNodes(ClassDescriptor, Set<String>, int, Map<?, ?>, List<String>, boolean) - Method in class org.intermine.web.struts.TreeController
Produce a list of tree nodes for a class and its children, marking as 'open' and recursing on any that appear on the openClasses list.
makePath(String) - Method in class org.intermine.pathquery.PathQuery
Produces a Path object from the given path String, using subclass information from the query.
makePathQuery(String, Collection<Integer>) - Method in class org.intermine.bio.webservice.AbstractRegionExportService
Make a path-query from a bag.
makePathQueryForBag(InterMineBag, WebConfig, Model) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
Create a PathQuery to get the contents of an InterMineBag
makePathQueryForCollection(WebConfig, ObjectStore, InterMineObject, String, String) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
Create a PathQuery to get results for a collection of items from an InterMineObject
makePublication(Integer) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Return the item identifier of the publication Item for the given pubmed id.
makeQuery(PathQuery, Map<String, InterMineBag>, Map<String, QuerySelectable>, BagQueryRunner, Map<String, BagQueryResult>) - Static method in class org.intermine.api.query.MainHelper
Converts a PathQuery object into an ObjectStore Query object, and optionally populates a Map from String path in the PathQuery to the object in the Query that represents it.
makeQuery(PathQuery) - Method in class org.intermine.api.query.PathQueryExecutor
Make the Lower-level Query object to run from the the higher level PathQuery one.
makeQuery(PathQuery) - Method in class org.intermine.api.query.QueryExecutor
Make an InterMine Query object from a PathQuery.
makeQuery(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor
Creates an IQL query from a PathQuery.
makeQuery(PathQuery, Map<String, BagQueryResult>, Map<String, QuerySelectable>) - Method in class org.intermine.api.query.WebResultsExecutor
Creates an IQL query from a PathQuery.
makeQueryDateConstraint(QueryField, PathConstraintAttribute) - Static method in class org.intermine.api.query.MainHelper
Make a SimpleConstraint for the given Date Constraint.
makeRangeConstraint(Queryable, QueryNode, PathConstraintRange) - Static method in class org.intermine.api.query.MainHelper
 
makeRangeConstraint(ConstraintOp, Range, ConstraintOptions, QueryField, QueryField, QueryClass) - Method in class org.intermine.api.query.range.AbstractHelper
Construct a constraint for an individual range, to be combined as per the ConstraintOptions.
makeSegment(String, Integer, Integer) - Static method in class org.intermine.webservice.server.jbrowse.Segment
 
makeSelectedNodes(String, String, Model, boolean, PathQuery, WebConfig, Map<String, List<FieldDescriptor>>, BagManager, Profile, ObjectStoreSummary) - Static method in class org.intermine.web.logic.querybuilder.ModelBrowserHelper
Finds the collection of MetadataNode objects that the model browser needs to display.
makeSequenceItem(GFF3Converter, String) - Method in class org.intermine.bio.dataconversion.GFF3SeqHandler
For the given GFF3Converter and sequence identifier, make a new sequence object.
makeSql(PathQuery) - Method in class org.intermine.api.query.PathQueryExecutor
Get the SQl that will be run on the database.
makeSql(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor
Creates an SQL query from a PathQuery.
makeSummaryQuery(PathQuery, Map<String, InterMineBag>, Map<String, QuerySelectable>, String, ObjectStore, Map<String, List<FieldDescriptor>>, BagQueryConfig, ProfileManager, boolean) - Static method in class org.intermine.api.query.MainHelper
Generate a query from a PathQuery, to summarise a particular column of results.
makeSummaryQuery(PathQuery, String, Map<String, InterMineBag>, Map<String, QuerySelectable>, BagQueryRunner) - Static method in class org.intermine.api.query.MainHelper
Generate a query from a PathQuery, to summarise a particular column of results.
makeSummaryQuery(PathQuery, String, Map<String, InterMineBag>, Map<String, QuerySelectable>, BagQueryRunner, boolean) - Static method in class org.intermine.api.query.MainHelper
Generate a query from a PathQuery, to summarise a particular column of results.
makeSummaryQuery(PathQuery, String, boolean) - Method in class org.intermine.api.query.QueryExecutor
Creates a query that returns the summary for a column in a PathQuery.
makeSummaryQuery(PathQuery, String) - Method in class org.intermine.api.query.QueryExecutor
 
makeSummaryQuery(PathQuery, String, String, boolean) - Method in class org.intermine.api.query.QueryExecutor
Creates a query that returns the summary for a column in a PathQuery, applying a filter at the database level.
makeUcscCompatible() - Method in class org.intermine.bio.web.struts.GFF3ExportForm
Return whether to make exported GFF3 compatible with UCSC genome browser.
makeWithDifferentBatchSize(int) - Method in class org.intermine.objectstore.query.ResultsBatches
Returns a new ResultsBatches object with a different batch size with some of the data already filled in.
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.model.ModelService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.query.QueryUploadService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.query.SavedQueryRetrievalService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.search.QuickSearch
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.template.AvailableTemplatesService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.template.SingleTemplateService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.user.DeregistrationService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.WebService
Make the XML output given the HttpResponse's PrintWriter.
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.widget.AvailableWidgetsService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService
 
makeXMLOutput(PrintWriter) - Method in class org.intermine.webservice.server.widget.GraphService
 
manager - Variable in class org.intermine.api.profile.Profile
 
map(List<Tag>) - Method in class org.intermine.api.profile.TagMapper
Safely transform a list of tags into a list of string, preserving type information.
map(Iterable<T>, Function<T, R>) - Static method in class org.intermine.webservice.server.core.ListFunctions
Transform a collection of things into a list of other things.
MAP_TEMPLATE - Static variable in class org.intermine.api.config.Constants
template to run to get map of values associated with this mine gene.organism --> gene.homologue.organism
MapListener<K,V> - Interface in org.intermine.webservice.server.jbrowse
 
mapLocation - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord
 
mappingExists(String, String) - Method in class org.intermine.api.profile.PreferencesManager
 
MappingUtil - Class in org.intermine.util
Useful utilities to do with mappings.
MappingUtilChecker<T> - Interface in org.intermine.util
Interface providing the capability to check partial mappings for validity for the MappingUtil.
marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.ListTrackBinding
Convert a ListTrack to XML and write XML to given writer.
marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.LoginTrackBinding
Convert a LoginTrack to XML and write XML to given writer.
marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.QueryTrackBinding
Convert a QueryTrack to XML and write XML to given writer.
marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.SearchTrackBinding
Convert a SearchTrack to XML and write XML to given writer.
marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.TemplateTrackBinding
Convert a TemplateTrack to XML and write XML to given writer.
marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.TrackManagerBinding
Convert all tracks to XML and write XML to given writer.
marshal(InterMineBag) - Method in class org.intermine.api.xml.InterMineBagBinding
Convert an InterMine bag to XML
marshal(InterMineBag, XMLStreamWriter) - Static method in class org.intermine.api.xml.InterMineBagBinding
Convert a InterMineIdBag to XML and write XML to given writer.
marshal(Profile, ObjectStore, XMLStreamWriter, int, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.xml.ProfileBinding
Convert a Profile to XML and write XML to given writer.
marshal(Profile, ObjectStore, XMLStreamWriter, boolean, boolean, boolean, boolean, boolean, boolean, int, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.xml.ProfileBinding
Convert a Profile to XML and write XML to given writer.
marshal(ProfileManager, XMLStreamWriter) - Static method in class org.intermine.api.xml.ProfileManagerBinding
Convert the contents of a ProfileManager to XML and write the XML to the given writer.
marshal(SavedQuery, XMLStreamWriter, int) - Static method in class org.intermine.api.xml.SavedQueryBinding
Convert a SavedQuery to XML and write XML to given writer.
marshal(SavedQuery, int) - Static method in class org.intermine.api.xml.SavedQueryBinding
Convert a TemplateQuery to XML
marshal(Profile) - Method in class org.intermine.api.xml.SharedBagBinding
Convert the shared bags to XML
marshal(Profile, XMLStreamWriter) - Static method in class org.intermine.api.xml.SharedBagBinding
Convert the bags shared to the profile given in input and write XML to given writer.
marshal(Tag, XMLStreamWriter) - Static method in class org.intermine.api.xml.TagBinding
Convert a Tag to XML and write XML to given writer.
marshal(PathQuery, String, String, int) - Static method in class org.intermine.pathquery.PathQueryBinding
Convert a PathQuery to XML.
marshal(PathQuery, String, String, XMLStreamWriter, int) - Static method in class org.intermine.pathquery.PathQueryBinding
Marshal to an XMLStreamWriter.
marshal(TemplateQuery, XMLStreamWriter, int) - Static method in class org.intermine.template.xml.TemplateQueryBinding
Convert a TemplateQuery to XML and write XML to given writer.
marshal(TemplateQuery, int) - Static method in class org.intermine.template.xml.TemplateQueryBinding
Convert a TemplateQuery to XML
marshal(Collection<FastPathObject>, Writer) - Method in class org.intermine.util.XmlBinding
Marshal a collection of objects to an XML file.
MassTaggingEvent - Class in org.intermine.api.search
A representation of a notification that multiple tags have been added to a profile, and that we do not (indeed cannot) know what they all are.
MassTaggingEvent() - Constructor for class org.intermine.api.search.MassTaggingEvent
 
MATCHES - Static variable in class org.intermine.metadata.ConstraintOp
Require that the two arguments match
matchesAreIssues() - Method in class org.intermine.api.bag.BagQuery
Return the flag passed to the constructor.
MatchingFieldConfigAction - Class in org.intermine.bio.chado.config
A ConfigAction that succeeds only if the value matches a pattern.
MAX - Static variable in class org.intermine.objectstore.query.QueryFunction
Maximum value of a number of rows
max - Variable in class org.intermine.objectstore.query.ResultsInfo
 
MAX - Static variable in class org.intermine.sql.query.Function
MAX(v) aggregate function - takes one operand.
MAX_BAG_INLINE_SIZE - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
The maximum size a bag in a BagConstraint can be before we consider using a temporary table instead.
MAX_CODE - Static variable in class org.intermine.pathquery.PathQuery
The highest code value a constraint may be assigned.
MAX_CONSTRAINTS - Static variable in class org.intermine.pathquery.PathQuery
The maximum number of coded constraints a PathQuery may hold.
MAX_HINT_DISPLAY - Static variable in class org.intermine.web.logic.help.HintManager
The maximum number of times a particular hint should be displayed in a session.
MAX_HITS - Static variable in class org.intermine.api.lucene.KeywordSearch
maximum number of hits returned
MAX_LINESETS - Static variable in class org.intermine.sql.precompute.OptimiserCache
Maximum number of cache linesets in the cache.
MAX_NOT_LOGGED_BAG_SIZE - Static variable in class org.intermine.web.logic.Constants
Maximum size a bag should have if the user is not logged in (to save memory)
MAX_ROWS - Static variable in class org.intermine.task.RunIqlQueryTask
 
maxLimit - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
maxOffset - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
maxP - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
maxQueryParseTime - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
maxSize - Variable in class org.intermine.objectstore.query.ResultsBatches
 
maxSummaryValues - Variable in class org.intermine.api.template.TemplateSummariser
 
maxTime - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
maxValues - Variable in class org.intermine.objectstore.ObjectStoreSummary
 
MemoryOutput - Class in org.intermine.webservice.server.output
Implementation of Output that saves data to memory.
MemoryOutput() - Constructor for class org.intermine.webservice.server.output.MemoryOutput
Constructor
MemoryQueryStore - Class in org.intermine.api.query
An in-memory implementation of a query store.
MemoryQueryStore(int) - Constructor for class org.intermine.api.query.MemoryQueryStore
 
merge(PrecomputedTable, Query, Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Finds all the possible uses of a given precomputed table in the query, and returns them as a Set of new Queries.
merge(ItemList...) - Method in class org.intermine.webservice.client.services.ListService
Merge one or more lists into a new list.
merge(ListService.ListOperationInfo, ItemList...) - Method in class org.intermine.webservice.client.services.ListService
Merge one or more lists into a new list.
merge(Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService
Merge one or more lists into a new list.
merge(ListService.ListOperationInfo, Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService
Merge one or more lists into a new list.
mergeAttributes(ClassDescriptor, ClassDescriptor) - Static method in class org.intermine.modelproduction.ModelMerger
Merge the attributes of a target model class descriptor original with the attributes present in class descriptor merge.
mergeClass(ClassDescriptor, ClassDescriptor, Model, Set<ClassDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger
Merge the attributes, collections and references from ClassDescriptor merge into the ClassDescriptor original.
mergeCollections(ClassDescriptor, ClassDescriptor) - Static method in class org.intermine.modelproduction.ModelMerger
Merge the collections of a target model class descriptor original with the collections present in class descriptor merge.
mergeGroupBy(PrecomputedTable, Query, Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Tries to match a PrecomputedTable with a GROUP BY clause to this query.
mergeModel(Model, Set<ClassDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger
'Merges' the information from the set of ClassDescriptors classes into the model target.
mergeModelFromFiles(File, List<File>, ModelParser) - Static method in class org.intermine.modelproduction.ModelFileMerger
Merges a model from a core model file and a list of additions files.
mergeMultiple(Set<PrecomputedTable>, Query, Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Iteratively calls merge on query with all the PrecomputedTables in a Set, returning the results in a Map from the PrecomputedTable to the Set that merge returns.
mergeProfiles(Profile, Profile) - Static method in class org.intermine.web.logic.profile.LoginHandler
Merge two profiles together.
mergeReferences(ClassDescriptor, ClassDescriptor) - Static method in class org.intermine.modelproduction.ModelMerger
Merge the references of a target model class descriptor original with the references present in class descriptor merge.
MergeSourceModelsTask - Class in org.intermine.task
Task to merge additions files from all sources in the project.xml into an intermine XML model.
MergeSourceModelsTask() - Constructor for class org.intermine.task.MergeSourceModelsTask
 
MessageFormat - Enum in org.intermine.web.struts.oauth2
 
MESSAGES - Static variable in class org.intermine.web.logic.Constants
Session attribute that temporarily holds a Vector of messages that will be displayed by the errorMessages.jsp on the next page viewed by the user and then removed (allows message after redirect).
MetabolicGeneSummaryDisplayer - Class in org.intermine.bio.web.displayer
 
MetabolicGeneSummaryDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer
Construct with config and the InterMineAPI.
MetabolicGeneSummaryDisplayer.GeneSummary - Class in org.intermine.bio.web.displayer
Internal wrapper.
MetabolicGeneSummaryDisplayer.GeneSummary(InterMineObject, HttpServletRequest) - Constructor for class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary
 
METADATA_TABLE - Static variable in class org.intermine.modelproduction.MetadataManager
Name of the metadata table (created by TorqueModelOutput)
MetaDataException - Exception in org.intermine.metadata
An Exception that may be thrown if metadata is in an invalid state.
MetaDataException() - Constructor for exception org.intermine.metadata.MetaDataException
Constructs an MetaDataException
MetaDataException(String) - Constructor for exception org.intermine.metadata.MetaDataException
Constructs an MetaDataException with the specified detail message.
MetaDataException(Throwable) - Constructor for exception org.intermine.metadata.MetaDataException
Constructs an MetaDataException with the specified nested throwable.
MetaDataException(String, Throwable) - Constructor for exception org.intermine.metadata.MetaDataException
Constructs an MetaDataException with the specified detail message and nested throwable.
MetadataManager - Class in org.intermine.modelproduction
Class to handle persistence of an intermine objectstore's metadata to the objectstore's database
MetadataManager.LargeObjectInputStream - Class in org.intermine.modelproduction
Class providing an InputStream interface to read a value from the database.
MetadataManager.LargeObjectInputStream(Connection, LargeObject) - Constructor for class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream
Constructor.
MetadataManager.LargeObjectInputStream(Connection, LargeObject, boolean) - Constructor for class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream
Constructor.
MetadataManager.LargeObjectOutputStream - Class in org.intermine.modelproduction
OutputStream class that writes to a large object in the database.
MetadataManager.LargeObjectOutputStream(Connection, LargeObject) - Constructor for class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream
Constructs a new object.
MetadataManager.LargeObjectOutputStream(Connection, LargeObject, boolean) - Constructor for class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream
Constructs a new object.
MetadataNode - Class in org.intermine.web.logic.query
Node used in displaying metadata
MetadataNode(String, List<String>, PathQuery, Map<String, List<FieldDescriptor>>, BagManager, Profile) - Constructor for class org.intermine.web.logic.query.MetadataNode
Constructor for a root node
MetadataNode(MetadataNode, String, String, List<String>, PathQuery, Map<String, List<FieldDescriptor>>, BagManager, Profile, Boolean) - Constructor for class org.intermine.web.logic.query.MetadataNode
Constructor for a non-root node
methodRefId - Variable in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder
 
MgiIdentifiersResolverFactory - Class in org.intermine.bio.dataconversion
ID resolver for MGI genes.
MgiIdentifiersResolverFactory() - Constructor for class org.intermine.bio.dataconversion.MgiIdentifiersResolverFactory
Construct without SO term of the feature type.
MgiIdentifiersResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.MgiIdentifiersResolverFactory
Construct with SO term of the feature type.
MicroArrayHelper - Class in org.flymine.web
Some static methods that query microarray data.
MigrationMapping - Class in org.intermine.web.struts.oauth2
A simple record that contains mapping information about the old id of a user.
MigrationMapping(String, String) - Constructor for class org.intermine.web.struts.oauth2.MigrationMapping
Construct a mapping for Google OpenID migration.
MIN - Static variable in class org.intermine.objectstore.query.QueryFunction
Mininum value of a number of rows
min - Variable in class org.intermine.objectstore.query.ResultsInfo
 
MIN - Static variable in class org.intermine.sql.query.Function
MIN(v) aggregate function - takes one operand.
MIN_CODE - Static variable in class org.intermine.pathquery.PathQuery
The lowest code value a constraint may be assigned.
MIN_LIMIT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
The smallest legal result size you can request
minBagTableSize - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
Mine - Interface in org.intermine.api.mines
The type of objects that represent InterMine instances.
MinePathwaysDisplayer - Class in org.intermine.bio.web.displayer
For all friendly mines, query for pathways
MinePathwaysDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.MinePathwaysDisplayer
Construct with config and the InterMineAPI.
MineRequester - Interface in org.intermine.api.mines
The type of objects that can request data from mines.
MinimalJsonIterator - Class in org.intermine.webservice.server.output
 
MinimalJsonIterator(Iterator<List<ResultElement>>) - Constructor for class org.intermine.webservice.server.output.MinimalJsonIterator
Constructor
minRows - Variable in class org.intermine.task.PrecomputeTask
 
minRows - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
minSize - Variable in class org.intermine.objectstore.query.ResultsBatches
 
MINUS - Static variable in class org.intermine.sql.query.Function
MINUS function - takes two operands.
MISSING_TABLES - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key used to store the missing tables string.
MissingParameterException - Exception in org.intermine.webservice.server.exceptions
 
MissingParameterException(String) - Constructor for exception org.intermine.webservice.server.exceptions.MissingParameterException
 
MissingParameterException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.MissingParameterException
 
MockIdResolverFactory - Class in org.intermine.bio.dataconversion
A mock IdResolver factory needed for testing.
MockIdResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.MockIdResolverFactory
Construct with class name for mock IdResolver
MockItemWriter - Class in org.intermine.dataconversion
Mimic behaviour of an ItemWriter but actually store Items in a Map rather than an ObjectStoreWriter
MockItemWriter(Map<String, Item>) - Constructor for class org.intermine.dataconversion.MockItemWriter
Constructor
MODE_NORMAL - Static variable in class org.intermine.sql.precompute.QueryOptimiserContext
Normal operation - no logging
MODE_VERBOSE - Static variable in class org.intermine.sql.precompute.QueryOptimiserContext
Normal operation, plus logging to stdout
MODE_VERBOSE_LIST - Static variable in class org.intermine.sql.precompute.QueryOptimiserContext
Logs all generated queries to the stdout, without explaining
MODE_VERBOSE_SUMMARY - Static variable in class org.intermine.sql.precompute.QueryOptimiserContext
Summarises all generated queries to the stdout, without explaining
model - Variable in class org.intermine.api.bag.operations.BagOperation
 
model - Variable in class org.intermine.api.InterMineAPI
 
model - Variable in class org.intermine.api.results.WebResults
 
model - Variable in class org.intermine.bio.task.GFF3ConverterTask
 
model - Variable in class org.intermine.codegen.JavaModelOutput
 
model - Variable in class org.intermine.dataconversion.ItemToObjectTranslator
 
model - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher
 
Model - Class in org.intermine.metadata
Represents a named business model, makes available metadata for each class within model.
Model(String, String, int, Collection<ClassDescriptor>) - Constructor for class org.intermine.metadata.Model
Construct a Model with a name and set of ClassDescriptors.
Model(String, String, Collection<ClassDescriptor>) - Constructor for class org.intermine.metadata.Model
Construct a model without a version.
MODEL - Static variable in class org.intermine.metadata.Util
Name of the key under which to store the serialized version of the model
MODEL - Static variable in class org.intermine.modelproduction.MetadataManager
Name of the key under which to store the serialized version of the model
model - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
model - Variable in class org.intermine.task.AnalyseDbTask
 
model - Variable in class org.intermine.task.ModelOutputTask
 
model - Variable in class org.intermine.util.XmlBinding
 
model - Variable in class org.intermine.web.logic.results.InlineResultsTable
 
model - Variable in class org.intermine.webservice.server.core.JSONService
 
Model.ModelAST - Class in org.intermine.metadata
A Map
Model.ModelAST() - Constructor for class org.intermine.metadata.Model.ModelAST
 
ModelBrowserHelper - Class in org.intermine.web.logic.querybuilder
Static class holding methods for managing the model browser in the query builder.
ModelBrowserHelper.NodeBuilder - Class in org.intermine.web.logic.querybuilder
An object that will descend through the model and build a tree of metadata nodes.
ModelBrowserHelper.NodeBuilder(boolean, PathQuery, Map<String, List<FieldDescriptor>>, BagManager, Profile, ObjectStoreSummary, WebConfig) - Constructor for class org.intermine.web.logic.querybuilder.ModelBrowserHelper.NodeBuilder
Construct a NodeBuilder
modelDescriptors - Static variable in class org.intermine.dataloader.DataLoaderHelper
 
ModelFactory - Class in org.intermine.metadata
A class that loads a model given a name.
ModelFileMerger - Class in org.intermine.modelproduction
Methods for merging a model from a list of files.
modelKeys - Static variable in class org.intermine.metadata.PrimaryKeyUtil
 
ModelMerger - Class in org.intermine.modelproduction
Merge model additions into a source model to produce a new larger model.
ModelMergerException - Exception in org.intermine.modelproduction
An Exception that may be thrown by ModelMerger methods.
ModelMergerException() - Constructor for exception org.intermine.modelproduction.ModelMergerException
Constructs a ModelMergerException
ModelMergerException(String) - Constructor for exception org.intermine.modelproduction.ModelMergerException
Constructs a ModelMergerException with the specified detail message.
ModelMergerException(Throwable) - Constructor for exception org.intermine.modelproduction.ModelMergerException
Constructs a ModelMergerException with the specified nested throwable.
ModelMergerException(String, Throwable) - Constructor for exception org.intermine.modelproduction.ModelMergerException
Constructs a ModelMergerException with the specified detail message and nested throwable.
ModelMergerTask - Class in org.intermine.task
Task to merge a single additions file into an intermine XML model.
ModelMergerTask() - Constructor for class org.intermine.task.ModelMergerTask
 
modelName - Variable in class org.intermine.task.StoreMetadataTask
 
ModelOutputTask - Class in org.intermine.task
Creates and runs a ModelOutput process to generate java or config files.
ModelOutputTask() - Constructor for class org.intermine.task.ModelOutputTask
 
ModelParser - Interface in org.intermine.metadata
Common interface for parsing source models into InterMine model format.
ModelParserException - Exception in org.intermine.metadata
An Exception that may be thrown by ModelMerger methods.
ModelParserException() - Constructor for exception org.intermine.metadata.ModelParserException
Constructs a ModelParserException
ModelParserException(String) - Constructor for exception org.intermine.metadata.ModelParserException
Constructs a ModelParserException with the specified detail message.
ModelParserException(Throwable) - Constructor for exception org.intermine.metadata.ModelParserException
Constructs a ModelParserException with the specified nested throwable.
ModelParserException(String, Throwable) - Constructor for exception org.intermine.metadata.ModelParserException
Constructs a ModelParserException with the specified detail message and nested throwable.
ModelService - Class in org.intermine.webservice.client.services
This class represents a connection to the RESTful resource on an InterMine server which provides information about the service's data model.
ModelService(String, String) - Constructor for class org.intermine.webservice.client.services.ModelService
Please do not instantiate this class yourself directly - instead use the ServiceFactory - this will ensure maintainability of your code.
ModelService - Class in org.intermine.webservice.server.model
Web service that returns a serialised representation of the data model.
ModelService(InterMineAPI) - Constructor for class org.intermine.webservice.server.model.ModelService
Constructor.
ModelServlet - Class in org.intermine.webservice.server.model
Runs ModelService web service.
ModelServlet() - Constructor for class org.intermine.webservice.server.model.ModelServlet
 
ModelUpdate - Class in org.intermine.api.profile
Update savedquery, savedtemplatequery and savedbag when the model has been changed
ModelUpdate(ObjectStore, ObjectStoreWriter, Model) - Constructor for class org.intermine.api.profile.ModelUpdate
Construct a ModelUpdate for updating items built in the userprofile with the oldModel given in input
ModelUpdateTask - Class in org.intermine.web.task
Task updating savedquery, savedtemplatequery and savedbag in the userprofile (identified by the userProfileAlias) when the model has been changed
ModelUpdateTask() - Constructor for class org.intermine.web.task.ModelUpdateTask
 
ModEncodeFeatureProcessor - Class in org.intermine.bio.dataconversion
A processor that loads feature referred to by the modENCODE metadata.
ModEncodeFeatureProcessor(ChadoDBConverter, String, String, String, String, String) - Constructor for class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Create a new ModEncodeFeatureProcessor.
ModEncodeMetaDataProcessor - Class in org.intermine.bio.dataconversion
Create items from the modENCODE metadata extensions to the chado schema.
ModEncodeMetaDataProcessor(ChadoDBConverter) - Constructor for class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Create a new ChadoProcessor object
ModifyBagAction - Class in org.intermine.web.struts
Implementation of Action to modify bags
ModifyBagAction() - Constructor for class org.intermine.web.struts.ModifyBagAction
 
ModifyBagDetailsAction - Class in org.intermine.web.struts
 
ModifyBagDetailsAction() - Constructor for class org.intermine.web.struts.ModifyBagDetailsAction
 
ModifyBagDetailsForm - Class in org.intermine.web.struts
 
ModifyBagDetailsForm() - Constructor for class org.intermine.web.struts.ModifyBagDetailsForm
Constructor
ModifyBagForm - Class in org.intermine.web.struts
Form bean to used in combining bags
ModifyBagForm() - Constructor for class org.intermine.web.struts.ModifyBagForm
Constructor
ModifyDetails - Class in org.intermine.web.struts
Action to handle events related to displaying Report templates and displayers
ModifyDetails() - Constructor for class org.intermine.web.struts.ModifyDetails
 
modifyList(Set<String>, InterMineBag) - Method in class org.intermine.webservice.server.lists.ListTagAddingService
Modify the list by adding the tags.
modifyList(Set<String>, InterMineBag) - Method in class org.intermine.webservice.server.lists.ListTagRemovalService
 
ModifyQueryAction - Class in org.intermine.web.struts
Action that results from a button press on the user profile page.
ModifyQueryAction() - Constructor for class org.intermine.web.struts.ModifyQueryAction
 
ModifyQueryChangeAction - Class in org.intermine.web.struts
Implementation of Action that modifies a saved query or bag.
ModifyQueryChangeAction() - Constructor for class org.intermine.web.struts.ModifyQueryChangeAction
 
ModifyQueryForm - Class in org.intermine.web.struts
Form bean to used in combining queries
ModifyQueryForm() - Constructor for class org.intermine.web.struts.ModifyQueryForm
Constructor
ModifySuperUserAction - Class in org.intermine.web.struts
Implementation of Action to modify superuser role
ModifySuperUserAction() - Constructor for class org.intermine.web.struts.ModifySuperUserAction
 
ModifySuperUserForm - Class in org.intermine.web.struts
Form bean used in user admin page
ModifySuperUserForm() - Constructor for class org.intermine.web.struts.ModifySuperUserForm
Constructor
ModifyTemplateAction - Class in org.intermine.web.struts
Action that results from a button press on the user profile page.
ModifyTemplateAction() - Constructor for class org.intermine.web.struts.ModifyTemplateAction
 
ModifyTemplateForm - Class in org.intermine.web.struts
Form bean used on the saved template form.
ModifyTemplateForm() - Constructor for class org.intermine.web.struts.ModifyTemplateForm
Constructor
MODMINE_METADATA_CACHE - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key used to store the modMine MetaData cache
MODULE_NAME - Static variable in class org.intermine.webservice.server.WebServiceConstants
Name of module of web services.
MODULO - Static variable in class org.intermine.objectstore.query.QueryExpression
Return the modulo of two expressions, e.g.
MODULO - Static variable in class org.intermine.sql.query.Function
MODULO arithmetic function - takes two operands.
MouseAllelesDisplayer - Class in org.intermine.bio.web.displayer
If we are mouse, fetch results straight off of us, otherwise create a PathQuery from other organisms.
MouseAllelesDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.MouseAllelesDisplayer
Construct with config and the InterMineAPI.
moveColumnLeft(int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Move a column left
moveColumnLeft(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction
Deprecated.
as we don't move columns any more
moveColumnRight(int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Move a column right
moveColumnRight(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction
Deprecated.
as we don't move columns any more
moveLeft(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderViewChange
Shift a Node left in the view
moveRight(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderViewChange
Shift a Node right in the view
moveToRequest(String, HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods
Move an attribute from the session to the request, removing it from the session.
MULTI_PART_FORM - Static variable in class org.intermine.webservice.client.core.ContentType
Content type for multi-part form requests.
MultiPartRequest - Class in org.intermine.webservice.client.core
A class for constructing multi-part form requests.
MultiPartRequest(String) - Constructor for class org.intermine.webservice.client.core.MultiPartRequest
Construct a new request to the given URL.
MultipleInBagConstraint - Class in org.intermine.objectstore.query
Constraint type requiring any of the given QueryEvaluables to be in a given bag.
MultipleInBagConstraint(Collection<?>, List<? extends QueryEvaluable>) - Constructor for class org.intermine.objectstore.query.MultipleInBagConstraint
Constructor for this class.
multipleInBagConstraintToString(SqlGenerator.State, StringBuffer, MultipleInBagConstraint, Query, int) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a BagConstraint object into a String suitable for putting on an SQL query.
MULTIPLY - Static variable in class org.intermine.objectstore.query.QueryExpression
Multiplication of two numeric fields
MULTIPLY - Static variable in class org.intermine.sql.query.Function
MULTIPLY function - takes two or more operands.
MultiRow<E> - Class in org.intermine.api.results.flatouterjoins
A subclass of ArrayList returned by the ResultsFlatOuterJoinsImpl indicating a row that can be represented as multiple rows because of collections.
MultiRow() - Constructor for class org.intermine.api.results.flatouterjoins.MultiRow
 
MultiRow(Collection<? extends E>) - Constructor for class org.intermine.api.results.flatouterjoins.MultiRow
 
MultiRowFirstValue<E> - Class in org.intermine.api.results.flatouterjoins
An object representing an entry in a MultiRow - the first instance of this value in a rowspan.
MultiRowFirstValue(E, int) - Constructor for class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
Constructor.
MultiRowLaterValue<E> - Class in org.intermine.api.results.flatouterjoins
An object representing an entry in a MultiRow - entries other than the first value of the rowspan.
MultiRowLaterValue(MultiRowFirstValue<E>) - Constructor for class org.intermine.api.results.flatouterjoins.MultiRowLaterValue
Constructor - should only really be called from MultiRowFirstValue.
MultiRowValue<E> - Class in org.intermine.api.results.flatouterjoins
An object representing an entry in a MultiRow.
MultiRowValue() - Constructor for class org.intermine.api.results.flatouterjoins.MultiRowValue
 
multiValueAttribute - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
MYMINE_PAGE - Static variable in class org.intermine.web.logic.Constants
Session attribute, name of tab selected on MyMine page.
MyMineController - Class in org.intermine.web.struts
Tiles controller for history tile (page).
MyMineController() - Constructor for class org.intermine.web.struts.MyMineController
 

N

n - Variable in class org.intermine.web.logic.query.QueryMonitorTimeout
Number of milliseconds before timeout.
N_ONE_RELATION - Static variable in class org.intermine.metadata.FieldDescriptor
A N:1 relationship.
name - Variable in class org.intermine.api.results.Column
 
name - Variable in class org.intermine.metadata.FieldDescriptor
 
name - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
name - Variable in class org.intermine.sql.query.Field
 
name - Variable in class org.intermine.sql.query.Table
 
name - Variable in class org.intermine.template.TemplateQuery
Template query name.
name - Variable in class org.intermine.util.ReferenceMap
 
name - Variable in class org.intermine.xml.full.ReferenceList
 
NAME_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
The name of the new list
NAME_PARAMETER - Static variable in class org.intermine.webservice.server.template.result.TemplateResultService
Name of name parameter
Names - Class in org.intermine.webservice.server.jbrowse
 
Names(InterMineAPI) - Constructor for class org.intermine.webservice.server.jbrowse.Names
 
NameSpacedProperties - Class in org.intermine.webservice.server.jbrowse.util
Class for simplifying access to sets of namespaces properties.
NameSpacedProperties(String, Properties) - Constructor for class org.intermine.webservice.server.jbrowse.util.NameSpacedProperties
Build a new name-spaced property set with a given parent set of properties, and the designated name-space.
namespaceToId - Variable in class org.intermine.dataconversion.ItemToObjectTranslator
 
nameToTerm - Variable in class org.intermine.bio.dataconversion.OboConverter
 
NameUtil - Class in org.intermine.api.util
Utility methods for naming queries and lists.
NAND - Static variable in class org.intermine.metadata.ConstraintOp
Combine constraints with the NAND operation
NavigationBarTag - Class in org.intermine.web.tags.table
Class implementing rendering of html of navigation bar.
NavigationBarTag() - Constructor for class org.intermine.web.tags.table.NavigationBarTag
 
NCBIFastaLoaderTask - Class in org.intermine.bio.dataconversion
A loader that works for FASTA files with an NCBI formatted header: http://www.ncbi.nlm.nih.gov/blast/fasta.shtml http://en.wikipedia.org/wiki/Fasta_format
NCBIFastaLoaderTask() - Constructor for class org.intermine.bio.dataconversion.NCBIFastaLoaderTask
 
NcbiGeneInfoParser - Class in org.intermine.bio.dataconversion
Parse NCBI Entrez gene_info file and return data structure for each row for later processing.
NcbiGeneInfoParser(Reader, Set<String>) - Constructor for class org.intermine.bio.dataconversion.NcbiGeneInfoParser
Construct the parser with the file to read, the input file can be for a single taxon or for multiple.
NcbiGffGFF3RecordHandler - Class in org.intermine.bio.dataconversion
A converter/retriever for the NcbiGff dataset via GFF files.
NcbiGffGFF3RecordHandler(Model) - Constructor for class org.intermine.bio.dataconversion.NcbiGffGFF3RecordHandler
Create a new NcbiGffGFF3RecordHandler for the given data model.
NcbiGffGFF3SeqHandler - Class in org.intermine.bio.dataconversion
A handler for NCBI GFF chromosomes
NcbiGffGFF3SeqHandler() - Constructor for class org.intermine.bio.dataconversion.NcbiGffGFF3SeqHandler
Construct the seq handler.
needsDistinct(Query) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Returns true if this query requires a DISTINCT keyword in the generated SQL.
negate() - Method in class org.intermine.api.query.range.ConstraintOptions
Return a new constraint set with each ConstraintOp negated.
negate() - Method in class org.intermine.metadata.ConstraintOp
Get the negated op
negate() - Method in class org.intermine.objectstore.query.Constraint
Negate this constraint. i.e equals becomes not equals.
negateAndSwap() - Method in class org.intermine.api.query.range.ConstraintOptions
Return a new constraint set with each ConstraintOp negated, and the left and right fields swapped.
NEGATIVE_SEGMENT - Static variable in class org.intermine.webservice.server.jbrowse.Segment
negative segment
neq(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be not equal to a value.
NEVER_EXPLAIN_TABLES - Static variable in class org.intermine.sql.precompute.BestQueryExplainer
 
NEW_NAME_PARAM - Static variable in class org.intermine.webservice.server.lists.ListRenameInput
The request parameter for the new name
NEW_TEMPLATE - Static variable in class org.intermine.web.logic.Constants
Session attribute used to store the status new template
newBagName - Variable in class org.intermine.web.struts.ModifyBagForm
 
newBagName - Variable in class org.intermine.web.struts.SaveBagForm
 
newBagType - Variable in class org.intermine.web.struts.TriageBagForm
 
newConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Add a new constraint to the query.
NewDeletionTokenService - Class in org.intermine.webservice.server.user
A service that issues a deletion token to a user who intends to delete their profile.
NewDeletionTokenService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.NewDeletionTokenService
 
newId(String) - Method in class org.intermine.dataconversion.DataConverter
Generate an identifier for an item, assign ids sequentially with a different alias per class, e.g.
newpassword - Variable in class org.intermine.web.struts.PasswordResetForm
 
newpassword2 - Variable in class org.intermine.web.struts.PasswordResetForm
 
newPathQuery - Variable in class org.intermine.api.profile.PathQueryUpdate
 
newQuery(String, HttpSession) - Static method in class org.intermine.web.struts.QueryClassSelectAction
Add a new query, based on the specified class, to the session.
newRef(Object, ReferenceQueue<Object>, K) - Method in class org.intermine.util.ReferenceMap
Private method to create a new ReferenceWithKey object.
newRef(Object, ReferenceQueue<Object>, K) - Method in class org.intermine.util.SoftReferenceMap
Returns a new SoftReferenceWithKey object for the given objects.
newRef(Object, ReferenceQueue<Object>, K) - Method in class org.intermine.util.WeakReferenceMap
Returns a new WeakReferenceWithKey object for the given objects.
NewUserService - Class in org.intermine.webservice.server.user
Service for creating a new user.
NewUserService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.NewUserService
Constructor.
NewUserServlet - Class in org.intermine.webservice.server.user
Servlet for handing off requests to the a NewUserService.
NewUserServlet() - Constructor for class org.intermine.webservice.server.user.NewUserServlet
 
next() - Method in class org.intermine.api.results.ExportResultsIterator
next() - Method in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator
next() - Method in class org.intermine.util.CombinedIterator
next() - Method in class org.intermine.util.ObjectPipe
next() - Method in class org.intermine.util.SynchronisedIterator
next() - Method in class org.intermine.webservice.client.results.Page
Get the next page.
next() - Method in class org.intermine.webservice.server.core.TableRowIterator
 
next() - Method in class org.intermine.webservice.server.output.FilteringResultIterator
 
next() - Method in class org.intermine.webservice.server.output.JSONDataTableRowIterator
 
next() - Method in class org.intermine.webservice.server.output.JSONResultsIterator
next() - Method in class org.intermine.webservice.server.output.JSONRowIterator
 
next() - Method in class org.intermine.webservice.server.output.MinimalJsonIterator
 
nextPage() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Go to the next page
NO_ALIASES_ALL_FIELDS - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
I DON'T KNOW
NO_BAGS - Static variable in class org.intermine.api.profile.Profile
Empty typed map holding no bags - useful when creating profiles.
NO_NOTXML - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key used to store the noNotXml string.
NO_QUERIES - Static variable in class org.intermine.api.profile.Profile
Empty typed map holding no saved queries - useful when creating profiles.
NO_SPAM - Static variable in class org.intermine.web.logic.Constants
The preference set if the user does not like lots of emails
NO_TEMPLATES - Static variable in class org.intermine.api.profile.Profile
Empty typed map holding no templates - useful when creating profiles.
NoContent - Exception in org.intermine.api.bag.operations
 
NoContent() - Constructor for exception org.intermine.api.bag.operations.NoContent
Constructor
NoContentException - Exception in org.intermine.webservice.server.exceptions
The NoContentException is thrown by a service when the resource requested exists but has an empty representation.
NoContentException(String) - Constructor for exception org.intermine.webservice.server.exceptions.NoContentException
 
NoContentException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.NoContentException
 
NoContentException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.NoContentException
 
Node - Class in org.intermine.pathquery
Superclass of left and right nodes
Node(String) - Constructor for class org.intermine.pathquery.Node
Constructor for a root node
Node(Node, String, boolean) - Constructor for class org.intermine.pathquery.Node
Constructor for a non-root node.
nodeToString(Query, Object, List<Object>, Set<QueryObjectPathExpression>) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Converts an Object into a String.
NONCES - Static variable in class org.intermine.web.logic.Constants
The replay-attack prevention nonces
NONE_OF - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is not one of a list of values
noneOfValues(String, Collection<String>) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be NOT ONE OF a collection of values.
NonFatalMetaDataException - Exception in org.intermine.metadata
An Exception that may be thrown if metadata is in an invalid state.
NonFatalMetaDataException() - Constructor for exception org.intermine.metadata.NonFatalMetaDataException
Constructs an MetaDataException
NonFatalMetaDataException(String) - Constructor for exception org.intermine.metadata.NonFatalMetaDataException
Constructs an MetaDataException with the specified detail message.
NonFatalMetaDataException(Throwable) - Constructor for exception org.intermine.metadata.NonFatalMetaDataException
Constructs an MetaDataException with the specified nested throwable.
NonFatalMetaDataException(String, Throwable) - Constructor for exception org.intermine.metadata.NonFatalMetaDataException
Constructs an MetaDataException with the specified detail message and nested throwable.
NonOverrideableProperties - Class in org.intermine.metadata
Subclass of java.util.Properties that rejects duplicate definitions of a given property.
NonOverrideableProperties() - Constructor for class org.intermine.metadata.NonOverrideableProperties
Empty constructor.
NonOverrideableProperties(Properties) - Constructor for class org.intermine.metadata.NonOverrideableProperties
Constructor with defaults.
NonUniqueName - Exception in org.intermine.api.bag.operations
Exception for non-unique name
NonUniqueName(String) - Constructor for exception org.intermine.api.bag.operations.NonUniqueName
 
NOR - Static variable in class org.intermine.metadata.ConstraintOp
Combine constraints with the NOR operation
NoServiceException - Exception in org.intermine.webservice.server.core
Exception to throw to signal that there is no service bound to a particular method on a particular endpoint.
NoServiceException() - Constructor for exception org.intermine.webservice.server.core.NoServiceException
 
NOT_ACCEPTABLE - Static variable in class org.intermine.webservice.server.output.Output
Request will only accept content in a format we cannot provide.
NOT_EQUAL - Static variable in class org.intermine.sql.query.AbstractValue
Describes one AbstractValue as being definitely not equal to another AbstractValue.
NOT_EQUALS - Static variable in class org.intermine.metadata.ConstraintOp
Require that the two arguments are not equal, ignoring case for strings
NOT_IN - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is NOT IN the second
NOT_RELATION - Static variable in class org.intermine.metadata.FieldDescriptor
Not a relationship between objects
NotAcceptableException - Exception in org.intermine.webservice.server.exceptions
 
NotAcceptableException() - Constructor for exception org.intermine.webservice.server.exceptions.NotAcceptableException
Construct a NotAcceptableException
notAnalysed - Variable in class org.intermine.web.logic.widget.Widget
 
NotConnectedException - Exception in org.intermine.webservice.client.exceptions
The NotConnectedException is thrown when some method requiring opened connection was called on closed HttpConnection.
NotConnectedException(String) - Constructor for exception org.intermine.webservice.client.exceptions.NotConnectedException
 
NotConnectedException() - Constructor for exception org.intermine.webservice.client.exceptions.NotConnectedException
Default constructor.
NotConstraint - Class in org.intermine.sql.query
A representation of a constraint that is represented here as the inverse of another Constraint.
NotConstraint(AbstractConstraint) - Constructor for class org.intermine.sql.query.NotConstraint
Constructor for a NotConstraint object.
NotCurrent - Exception in org.intermine.api.bag.operations
 
NotCurrent() - Constructor for exception org.intermine.api.bag.operations.NotCurrent
Constructor
notEqualTo(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
Compare this value of this AbstractValue with another to see if it is not equal.
notEqualToLoop(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be not equal to a loopPath.
NotImplementedException - Exception in org.intermine.webservice.client.exceptions
The NotImplementedException is thrown by a service when an attempt is made to send a request that is not supported by the target service.
NotImplementedException(String) - Constructor for exception org.intermine.webservice.client.exceptions.NotImplementedException
 
NotImplementedException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.NotImplementedException
 
NotImplementedException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.NotImplementedException
 
NotImplementedException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.NotImplementedException
 
NotImplementedException - Exception in org.intermine.webservice.server.exceptions
 
NotImplementedException(Class<?>, String) - Constructor for exception org.intermine.webservice.server.exceptions.NotImplementedException
 
notIn(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be NOT IN a named bag.
notInIds(String, Collection<Integer>) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be NOT IN a collection of ids.
notLike(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be NOT LIKE a value.
NotPresentException - Exception in org.intermine.api.query
 
NotPresentException(String) - Constructor for exception org.intermine.api.query.NotPresentException
 
NotXmlParser - Class in org.intermine.objectstore.intermine
Parses a String suitable for storing in the OBJECT field of database tables into an Object.
NotXmlRenderer - Class in org.intermine.objectstore.intermine
Render on object into a String suitable for storing in the OBJECT field of database tables.
NULL_MODEL_ITEM_FACTORY - Static variable in class org.intermine.xml.full.ItemFactory
An ItemFactory constructed with no Model, so the Items it creates do no type checking.
NULL_QUERY - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
NULL_QUERY - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
 
NULL_QUERY - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
NULL_VALUE - Static variable in class org.intermine.util.ReferenceMap
 
nullConstraint - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
NullFirstComparator - Class in org.intermine.util
A Comparator that uses the natural ordering of elements implementing Comparable, plus null is allowed and always before all other elements.
NullMailer - Class in org.intermine.web.context
An emailer that doesn't send emails, but does log what it has been asked to do.
NullMailer() - Constructor for class org.intermine.web.context.NullMailer
Get a new NullMailer
NullMailer(Properties) - Constructor for class org.intermine.web.context.NullMailer
Get a null mailer with certain properties.
NUMBER_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint
 

O

OAUTH2_PROVIDERS - Static variable in class org.intermine.web.logic.Constants
The key under which OAuth2 providers are stored
OAuthProvider - Interface in org.intermine.web.struts.oauth2
A description of an OAuth Provider that we can use as a source of identity information.
obj - Variable in class org.intermine.objectstore.query.ClassConstraint
 
obj - Variable in class org.intermine.objectstore.query.ContainsConstraint
 
obj - Variable in class org.intermine.objectstore.query.QueryFunction
 
ObjectDescription - Class in org.intermine.dataloader
Object class used by DataTracker for data tracking.
ObjectDescription() - Constructor for class org.intermine.dataloader.ObjectDescription
Constructs a new ObjectDescription.
ObjectDescription(ObjectDescription) - Constructor for class org.intermine.dataloader.ObjectDescription
Constructs a new ObjectDescription from an existing one.
ObjectDetails - Class in org.intermine.api.beans
An object that describes an object.
ObjectDetails() - Constructor for class org.intermine.api.beans.ObjectDetails
 
ObjectDetailsBeanInfo - Class in org.intermine.api.beans
An object that describes the ObjectDetails bean and supports DWR serialization.
ObjectDetailsBeanInfo() - Constructor for class org.intermine.api.beans.ObjectDetailsBeanInfo
 
ObjectFormatter - Class in org.intermine.webservice.server.jbrowse.util
Simpler version of JSONFormatter that doesn't add any extra information, except in case of error.
ObjectFormatter() - Constructor for class org.intermine.webservice.server.jbrowse.util.ObjectFormatter
 
ObjectPipe<E> - Class in org.intermine.util
This is a rather simple implementation of a queue designed for passing objects from one Thread to another to form a pipeline.
ObjectPipe() - Constructor for class org.intermine.util.ObjectPipe
Construct an ObjectPipe with a default maximum buffer size.
ObjectPipe(int) - Constructor for class org.intermine.util.ObjectPipe
Construct an ObjectPipe with a certain maximum buffer size.
objectPrimaryKeyNotNull(Model, InterMineObject, ClassDescriptor, PrimaryKey, Source, IntToIntMap) - Static method in class org.intermine.dataloader.DataLoaderHelper
Look a the values of the given primary key in the object and return true if and only if some part of the primary key is null.
ObjectRequest - Class in org.intermine.api.mines
A generic container for a request for information about an object.
ObjectRequest(String, String) - Constructor for class org.intermine.api.mines.ObjectRequest
Define a new object request.
Objects - Class in org.intermine.api.data
Helper class to encapsulate some common logic regarding the use of data objects.
objectStore - Variable in class org.intermine.api.InterMineAPI
 
ObjectStore - Interface in org.intermine.objectstore
Gets the Results of a Query from an underlying store.
ObjectStoreAbstractImpl - Class in org.intermine.objectstore
Abstract implementation of the ObjectStore interface.
ObjectStoreAbstractImpl() - Constructor for class org.intermine.objectstore.ObjectStoreAbstractImpl
No-arg constructor for testing purposes
ObjectStoreAbstractImpl(Model) - Constructor for class org.intermine.objectstore.ObjectStoreAbstractImpl
Construct an ObjectStore with some metadata
ObjectStoreBag - Class in org.intermine.objectstore.query
Object representing a collection of objects which have been stored in the database.
ObjectStoreBag(int) - Constructor for class org.intermine.objectstore.query.ObjectStoreBag
Constructs a new ObjectStoreBag.
ObjectStoreBagCombination - Class in org.intermine.objectstore.query
Object representing a combination of ObjectStoreBags.
ObjectStoreBagCombination(int) - Constructor for class org.intermine.objectstore.query.ObjectStoreBagCombination
Constructs a new ObjectStoreBagCombination.
ObjectStoreBagsForObject - Class in org.intermine.objectstore.query
Object representing a query to fetch ObjectStoreBag IDs for ObjectStoreBags that contain a certain value.
ObjectStoreBagsForObject(Integer) - Constructor for class org.intermine.objectstore.query.ObjectStoreBagsForObject
Constructs a new ObjectStoreBagsForObject with no limit on the ObjectStoreBags returned.
ObjectStoreBagsForObject(Integer, Collection<ObjectStoreBag>) - Constructor for class org.intermine.objectstore.query.ObjectStoreBagsForObject
Constructs a new ObjectStoreBagsForObject with a limited set of ObjectStoreBags that can be present in the results.
ObjectStoreDataLoader - Class in org.intermine.dataloader
Loads information from an ObjectStore into the InterMine database.
ObjectStoreDataLoader(IntegrationWriter) - Constructor for class org.intermine.dataloader.ObjectStoreDataLoader
Construct an ObjectStoreDataLoader
ObjectStoreDataLoaderTask - Class in org.intermine.dataloader
Uses an IntegrationWriter to load data from another ObjectStore.
ObjectStoreDataLoaderTask() - Constructor for class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
ObjectStoreException - Exception in org.intermine.objectstore
An Exception that may be thrown by an ObjectStore indicating a fatal error.
ObjectStoreException() - Constructor for exception org.intermine.objectstore.ObjectStoreException
Constructs an ObjectStoreException
ObjectStoreException(String) - Constructor for exception org.intermine.objectstore.ObjectStoreException
Constructs an ObjectStoreException with the specified detail message.
ObjectStoreException(Throwable) - Constructor for exception org.intermine.objectstore.ObjectStoreException
Constructs an ObjectStoreException with the specified nested throwable.
ObjectStoreException(String, Throwable) - Constructor for exception org.intermine.objectstore.ObjectStoreException
Constructs an ObjectStoreException with the specified detail message and nested throwable.
ObjectStoreFactory - Class in org.intermine.objectstore
Produce ObjectStores
ObjectStoreFastCollectionsForTranslatorImpl - Class in org.intermine.objectstore.fastcollections
Provides an implementation of an objectstore that explicitly materialises all the collections in the results set it provides, written for the translating objectstore.
ObjectStoreFastCollectionsForTranslatorImpl(ObjectStore) - Constructor for class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Creates an instance, from another ObjectStore instance.
ObjectStoreFastCollectionsImpl - Class in org.intermine.objectstore.fastcollections
Provides an implementation of an objectstore that explicitly materialises all the collections in the results set it provides.
ObjectStoreFastCollectionsImpl(ObjectStore) - Constructor for class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Creates an instance, from another ObjectStore instance.
ObjectStoreInterMineImpl - Class in org.intermine.objectstore.intermine
An SQL-backed implementation of the ObjectStore interface.
ObjectStoreInterMineImpl(Model) - Constructor for class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Constructs an ObjectStoreInterMineImpl - for use by the ObjectStoreWriter only!
ObjectStoreInterMineImpl(Database, DatabaseSchema) - Constructor for class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Constructs an ObjectStoreInterMineImpl, with a schema.
ObjectStoreInterMineImpl.BagTableToRemove - Class in org.intermine.objectstore.intermine
Class describing a temporary bag table, which can be removed.
ObjectStoreItemWriter - Class in org.intermine.dataconversion
Stores Items in an objectstore.
ObjectStoreItemWriter(ObjectStoreWriter) - Constructor for class org.intermine.dataconversion.ObjectStoreItemWriter
Constructs the ItemWriter with an ObjectStoreWriter.
ObjectStoreLimitReachedException - Exception in org.intermine.objectstore
An exception that may be thrown by the objectstore, when an access is made outside the allowable maximum query size.
ObjectStoreLimitReachedException() - Constructor for exception org.intermine.objectstore.ObjectStoreLimitReachedException
Constructs an ObjectStoreLimitReachedException.
ObjectStoreLimitReachedException(String) - Constructor for exception org.intermine.objectstore.ObjectStoreLimitReachedException
Constructs an ObjectStoreLimitReachedException with the specified detail message.
ObjectStorePassthruImpl - Class in org.intermine.objectstore
A generic ObjectStore that passes through every request to an underlying ObjectStore.
ObjectStorePassthruImpl(ObjectStore) - Constructor for class org.intermine.objectstore.ObjectStorePassthruImpl
Creates an instance, from another ObjectStore instance.
ObjectStoreQueryDurationException - Exception in org.intermine.objectstore
An Exception thrown if the estimated time to complete a query is greater than the maximum permitted.
ObjectStoreQueryDurationException() - Constructor for exception org.intermine.objectstore.ObjectStoreQueryDurationException
Create a new ObjectStoreQueryDurationException.
ObjectStoreQueryDurationException(String) - Constructor for exception org.intermine.objectstore.ObjectStoreQueryDurationException
Create a new ObjectStoreQueryDurationException with the given detail message.
ObjectStoreQueryDurationException(Throwable) - Constructor for exception org.intermine.objectstore.ObjectStoreQueryDurationException
Create a new ObjectStoreQueryDurationException with the specified nested throwable.
ObjectStoreQueryDurationException(String, Throwable) - Constructor for exception org.intermine.objectstore.ObjectStoreQueryDurationException
Create a new ObjectStoreQueryDurationException with the specified detail message and nested throwable.
ObjectStoreSafeImpl - Class in org.intermine.objectstore.safe
Provides a safe implementation of an objectstore - that is, an implementation that works correctly if passed a Query object that has been modified since being used previously.
ObjectStoreSafeImpl(ObjectStore) - Constructor for class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Creates an instance, from another ObjectStore instance.
ObjectStoreSummary - Class in org.intermine.objectstore
A summary of the data in an ObjectStore
ObjectStoreSummary(ObjectStore, Properties) - Constructor for class org.intermine.objectstore.ObjectStoreSummary
Construct a summary from by running queries in the ObjectStore.
ObjectStoreSummary(Properties) - Constructor for class org.intermine.objectstore.ObjectStoreSummary
Construct a summary from a properties object.
ObjectStoreTranslatingImpl - Class in org.intermine.objectstore.translating
ObjectStore that transparently translates incoming queries and outgoing objects
ObjectStoreTranslatingImpl(Model, ObjectStore, Translator) - Constructor for class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Constructor
objectStoreWriter - Variable in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask
 
objectStoreWriter - Variable in class org.intermine.bio.postprocess.PostProcessOperationsTask
 
ObjectStoreWriter - Interface in org.intermine.objectstore
Store, update, and delete objects
ObjectStoreWriterFactory - Class in org.intermine.objectstore
Produce ObjectStoreWriters
ObjectStoreWriterInterMineImpl - Class in org.intermine.objectstore.intermine
An SQL-backed implementation of the ObjectStoreWriter interface, backed by ObjectStoreInterMineImpl.
ObjectStoreWriterInterMineImpl(ObjectStore) - Constructor for class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Constructor for this ObjectStoreWriter.
objectToString(StringBuffer, Object) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts an Object to a String, in a form suitable for SQL.
objectToString(Object) - Static method in class org.intermine.sql.DatabaseUtil
Generate an SQL compatible representation of an object.
ObjectTrailController - Class in org.intermine.web.struts
Controller for the object trail tile.
ObjectTrailController() - Constructor for class org.intermine.web.struts.ObjectTrailController
 
ObjectTrailController.TrailElement - Class in org.intermine.web.struts
Bean passed to JSP to represent an element in the trail.
ObjectViewController - Class in org.intermine.web.struts
Controls display of data in results tables.
ObjectViewController() - Constructor for class org.intermine.web.struts.ObjectViewController
 
OboConverter - Class in org.intermine.bio.dataconversion
Convert tree of OboTerms into Items.
OboConverter(ItemWriter, Model, String, String, String, String) - Constructor for class org.intermine.bio.dataconversion.OboConverter
Constructor for this class.
OboConverterTask - Class in org.intermine.bio.task
Initiates retrieval and conversion of data from a source database
OboConverterTask() - Constructor for class org.intermine.bio.task.OboConverterTask
 
OboParser - Class in org.intermine.bio.ontology
 
OboParser() - Constructor for class org.intermine.bio.ontology.OboParser
 
OboRelation - Class in org.intermine.bio.ontology
Object representing an OBO relation.
OboRelation(String, String, OboTypeDefinition) - Constructor for class org.intermine.bio.ontology.OboRelation
Constructor
oboRelations - Variable in class org.intermine.bio.dataconversion.OboConverter
 
OboTerm - Class in org.intermine.bio.ontology
Extension of DagTerm that adds a namespace attribute that is specific to the OBO format.
OboTerm(String, String) - Constructor for class org.intermine.bio.ontology.OboTerm
Construct with an id and name.
OboTerm(String) - Constructor for class org.intermine.bio.ontology.OboTerm
Construct with an id, only used for uberon xrefs
oboTerms - Variable in class org.intermine.bio.dataconversion.OboConverter
 
OboTermSynonym - Class in org.intermine.bio.ontology
Object representing aa OboTerm synonym.
OboTermSynonym(String, String) - Constructor for class org.intermine.bio.ontology.OboTermSynonym
Create a new instance of DagTermSynonym.
OboTypeDefinition - Class in org.intermine.bio.ontology
Class representing an OBO type.
OboTypeDefinition(String, String, boolean) - Constructor for class org.intermine.bio.ontology.OboTypeDefinition
The constructor
officialName - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord
 
officialSymbol - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord
 
offset - Variable in class org.intermine.objectstore.query.ClobAccess
 
offset - Variable in class org.intermine.sql.query.Query
 
OLD - Static variable in class org.intermine.api.profile.ModelUpdate
suffix used to rename the previous items
OLD_NAME_PARAM - Static variable in class org.intermine.webservice.server.lists.ListRenameInput
The request parameter for the old name
oldModel - Variable in class org.intermine.api.profile.PathQueryUpdate
 
omit - Variable in class org.intermine.task.InheritanceDotTask
 
onData(Map<String, Object>, boolean) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
onData(Map.Entry<String, Object>, boolean) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
ONE - Static variable in class org.intermine.web.logic.widget.ErrorCorrection
 
ONE_N_RELATION - Static variable in class org.intermine.metadata.FieldDescriptor
A 1:N relationship.
ONE_OF - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is one of a list a values
ONE_ONE_RELATION - Static variable in class org.intermine.metadata.FieldDescriptor
A 1:1 relationship
oneOfValues(String, Collection<String>) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be ONE OF a collection of values.
ONTOLOGIES - Static variable in class org.intermine.bio.web.displayer.GeneOntologyDisplayer
The names of ontology root terms.
ontology - Variable in class org.intermine.bio.dataconversion.OboConverter
 
OntologyIdResolverFactory - Class in org.intermine.bio.dataconversion
 
OntologyIdResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.OntologyIdResolverFactory
Construct with SO term of the feature type to read from chado database.
op - Variable in class org.intermine.objectstore.query.Constraint
 
op - Variable in class org.intermine.objectstore.query.QueryFunction
 
op - Variable in class org.intermine.pathquery.PathConstraint
 
OPENID_PROVIDERS - Static variable in class org.intermine.web.logic.Constants
The key for the open-id providers located in the servlet context.
OpenIDAuthenticator - Class in org.intermine.web.logic.login
Authenticate requests using OpenID
OpenIDAuthenticator() - Constructor for class org.intermine.web.logic.login.OpenIDAuthenticator
Default constructor.
openResource(String) - Method in class org.intermine.web.logic.ClassResourceOpener
 
openResource(String) - Method in interface org.intermine.web.logic.ResourceOpener
Open a resource by name, and return an InputStream to it.
openResource(String) - Method in class org.intermine.web.struts.ResourceFinder
 
operands - Variable in class org.intermine.sql.query.Function
 
operate() - Method in class org.intermine.api.bag.operations.BagOperation
Perform this bag operation.
operate() - Method in interface org.intermine.api.bag.operations.BagProducer
 
operation - Variable in class org.intermine.bio.postprocess.PostProcessOperationsTask
 
operation - Variable in class org.intermine.sql.query.Constraint
 
operation - Variable in class org.intermine.sql.query.Function
 
operationButton - Variable in class org.intermine.web.struts.SaveBagForm
 
operator - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
OPPOSITE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints as being opposite to each other.
optimise - Variable in class org.intermine.objectstore.query.Results
 
optimise(String, Database) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Runs the optimiser through the query represented in the String, given the database.
optimise(String, Database, QueryOptimiserContext) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Runs the optimiser through the query represented in the String, given the database.
optimise(Query, Database) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Runs the optimiser through the query, given the database.
optimise(Query, Database, QueryOptimiserContext) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Runs the optimiser through the query, given the database.
optimise(String, Query, Object, Connection, QueryOptimiserContext) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Runs the optimiser through the query represented in the String and Query, given the Connection and an object to lookup a PrecomputedTable
OptimiserCache - Class in org.intermine.sql.precompute
A class that provides an implementation of a cache for String-based SQL query optimisation.
OptimiserCache() - Constructor for class org.intermine.sql.precompute.OptimiserCache
Constructor for this object.
OptimiserCacheLine - Class in org.intermine.sql.precompute
A class that provides an implementation of a cache line, encapsulating several pieces of data.
OptimiserCacheLine(String, int, String) - Constructor for class org.intermine.sql.precompute.OptimiserCacheLine
Constructor for this object.
OptimiserMappingChecker - Class in org.intermine.sql.precompute
Class for checking partial mappings for validity for the MappingUtil.
OptimiserMappingChecker(Set<AbstractConstraint>, Set<AbstractConstraint>) - Constructor for class org.intermine.sql.precompute.OptimiserMappingChecker
Constructor.
optimiseWith(String, Query, Database, Connection, QueryOptimiserContext, Set<PrecomputedTable>, OptimiserCache) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Runs the optimiser through the query repesented in the String and Query, given the Connection and a set of PrecomputedTables.
OR - Static variable in class org.intermine.metadata.ConstraintOp
Combine constraints with the OR operation
OR - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints as following "constraint 1 OR constraint 2 IS TRUE".
orderBags(Map<String, InterMineBag>) - Method in class org.intermine.api.bag.BagManager
Order a map of bags by im:order:n tag
orderBy - Variable in class org.intermine.sql.query.Query
 
ORDERBY_FIELD - Static variable in class org.intermine.sql.precompute.PrecomputedTable
The name of the field that is generated as the order by field
orderByField - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
OrderDescending - Class in org.intermine.objectstore.query
An element that can appear in the ORDER BY clause of a query, to reverse the order.
OrderDescending(QueryOrderable) - Constructor for class org.intermine.objectstore.query.OrderDescending
Creates a new OrderDescending object from the given QueryOrderable.
OrderDescending - Class in org.intermine.sql.query
A representation of an item that can be present in the ORDER BY section of an SQL query, but ordered descending..
OrderDescending(AbstractValue) - Constructor for class org.intermine.sql.query.OrderDescending
Constructor for OrderDescending.
OrderDirection - Enum in org.intermine.pathquery
An enumeration for the direction of sorting for results.
OrderElement - Class in org.intermine.pathquery
An element of the order by list of a PathQuery, containing a path and a direction.
OrderElement(String, OrderDirection) - Constructor for class org.intermine.pathquery.OrderElement
Constructor, taking a path and a direction.
org.flymine.web - package org.flymine.web
 
org.flymine.web.displayer - package org.flymine.web.displayer
 
org.intermine - package org.intermine
 
org.intermine.api - package org.intermine.api
 
org.intermine.api.bag - package org.intermine.api.bag
 
org.intermine.api.bag.operations - package org.intermine.api.bag.operations
 
org.intermine.api.beans - package org.intermine.api.beans
 
org.intermine.api.config - package org.intermine.api.config
 
org.intermine.api.data - package org.intermine.api.data
 
org.intermine.api.idresolution - package org.intermine.api.idresolution
 
org.intermine.api.lucene - package org.intermine.api.lucene
 
org.intermine.api.mines - package org.intermine.api.mines
 
org.intermine.api.profile - package org.intermine.api.profile
 
org.intermine.api.query - package org.intermine.api.query
 
org.intermine.api.query.codegen - package org.intermine.api.query.codegen
 
org.intermine.api.query.range - package org.intermine.api.query.range
 
org.intermine.api.results - package org.intermine.api.results
 
org.intermine.api.results.flatouterjoins - package org.intermine.api.results.flatouterjoins
 
org.intermine.api.search - package org.intermine.api.search
 
org.intermine.api.tag - package org.intermine.api.tag
 
org.intermine.api.template - package org.intermine.api.template
 
org.intermine.api.tracker - package org.intermine.api.tracker
 
org.intermine.api.tracker.factory - package org.intermine.api.tracker.factory
 
org.intermine.api.tracker.track - package org.intermine.api.tracker.track
 
org.intermine.api.tracker.util - package org.intermine.api.tracker.util
 
org.intermine.api.tracker.xml - package org.intermine.api.tracker.xml
 
org.intermine.api.types - package org.intermine.api.types
 
org.intermine.api.util - package org.intermine.api.util
 
org.intermine.api.xml - package org.intermine.api.xml
 
org.intermine.bio.chado - package org.intermine.bio.chado
 
org.intermine.bio.chado.config - package org.intermine.bio.chado.config
 
org.intermine.bio.dataconversion - package org.intermine.bio.dataconversion
 
org.intermine.bio.io.bed - package org.intermine.bio.io.bed
 
org.intermine.bio.io.gaf - package org.intermine.bio.io.gaf
 
org.intermine.bio.io.gff3 - package org.intermine.bio.io.gff3
 
org.intermine.bio.ontology - package org.intermine.bio.ontology
 
org.intermine.bio.postprocess - package org.intermine.bio.postprocess
 
org.intermine.bio.query.range - package org.intermine.bio.query.range
 
org.intermine.bio.task - package org.intermine.bio.task
 
org.intermine.bio.util - package org.intermine.bio.util
 
org.intermine.bio.web - package org.intermine.bio.web
 
org.intermine.bio.web.biojava - package org.intermine.bio.web.biojava
 
org.intermine.bio.web.displayer - package org.intermine.bio.web.displayer
 
org.intermine.bio.web.export - package org.intermine.bio.web.export
 
org.intermine.bio.web.logic - package org.intermine.bio.web.logic
 
org.intermine.bio.web.model - package org.intermine.bio.web.model
 
org.intermine.bio.web.struts - package org.intermine.bio.web.struts
 
org.intermine.bio.web.widget - package org.intermine.bio.web.widget
 
org.intermine.bio.webservice - package org.intermine.bio.webservice
 
org.intermine.codegen - package org.intermine.codegen
 
org.intermine.dataconversion - package org.intermine.dataconversion
 
org.intermine.dataloader - package org.intermine.dataloader
 
org.intermine.dwr - package org.intermine.dwr
 
org.intermine.metadata - package org.intermine.metadata
 
org.intermine.model - package org.intermine.model
 
org.intermine.model.testmodel.query.range - package org.intermine.model.testmodel.query.range
 
org.intermine.model.testmodel.web - package org.intermine.model.testmodel.web
 
org.intermine.model.testmodel.web.widget - package org.intermine.model.testmodel.web.widget
 
org.intermine.modelproduction - package org.intermine.modelproduction
 
org.intermine.objectstore - package org.intermine.objectstore
 
org.intermine.objectstore.fastcollections - package org.intermine.objectstore.fastcollections
 
org.intermine.objectstore.intermine - package org.intermine.objectstore.intermine
 
org.intermine.objectstore.proxy - package org.intermine.objectstore.proxy
 
org.intermine.objectstore.query - package org.intermine.objectstore.query
 
org.intermine.objectstore.query.iql - package org.intermine.objectstore.query.iql
 
org.intermine.objectstore.querygen - package org.intermine.objectstore.querygen
 
org.intermine.objectstore.safe - package org.intermine.objectstore.safe
 
org.intermine.objectstore.translating - package org.intermine.objectstore.translating
 
org.intermine.pathquery - package org.intermine.pathquery
 
org.intermine.postprocess - package org.intermine.postprocess
 
org.intermine.sql - package org.intermine.sql
 
org.intermine.sql.logging - package org.intermine.sql.logging
 
org.intermine.sql.precompute - package org.intermine.sql.precompute
 
org.intermine.sql.query - package org.intermine.sql.query
 
org.intermine.sql.writebatch - package org.intermine.sql.writebatch
 
org.intermine.task - package org.intermine.task
 
org.intermine.task.project - package org.intermine.task.project
 
org.intermine.template - package org.intermine.template
 
org.intermine.template.xml - package org.intermine.template.xml
 
org.intermine.util - package org.intermine.util
 
org.intermine.web.autocompletion - package org.intermine.web.autocompletion
 
org.intermine.web.bag - package org.intermine.web.bag
 
org.intermine.web.commandline - package org.intermine.web.commandline
 
org.intermine.web.context - package org.intermine.web.context
 
org.intermine.web.displayer - package org.intermine.web.displayer
 
org.intermine.web.filters - package org.intermine.web.filters
 
org.intermine.web.logic - package org.intermine.web.logic
 
org.intermine.web.logic.aspects - package org.intermine.web.logic.aspects
 
org.intermine.web.logic.bag - package org.intermine.web.logic.bag
 
org.intermine.web.logic.config - package org.intermine.web.logic.config
 
org.intermine.web.logic.export - package org.intermine.web.logic.export
 
org.intermine.web.logic.export.http - package org.intermine.web.logic.export.http
 
org.intermine.web.logic.export.rowformatters - package org.intermine.web.logic.export.rowformatters
 
org.intermine.web.logic.export.string - package org.intermine.web.logic.export.string
 
org.intermine.web.logic.help - package org.intermine.web.logic.help
 
org.intermine.web.logic.login - package org.intermine.web.logic.login
 
org.intermine.web.logic.pathqueryresult - package org.intermine.web.logic.pathqueryresult
 
org.intermine.web.logic.profile - package org.intermine.web.logic.profile
 
org.intermine.web.logic.query - package org.intermine.web.logic.query
 
org.intermine.web.logic.querybuilder - package org.intermine.web.logic.querybuilder
 
org.intermine.web.logic.results - package org.intermine.web.logic.results
 
org.intermine.web.logic.session - package org.intermine.web.logic.session
 
org.intermine.web.logic.template - package org.intermine.web.logic.template
 
org.intermine.web.logic.widget - package org.intermine.web.logic.widget
 
org.intermine.web.logic.widget.config - package org.intermine.web.logic.widget.config
 
org.intermine.web.search - package org.intermine.web.search
 
org.intermine.web.security - package org.intermine.web.security
 
org.intermine.web.struts - package org.intermine.web.struts
 
org.intermine.web.struts.oauth2 - package org.intermine.web.struts.oauth2
 
org.intermine.web.tags.disclosure - package org.intermine.web.tags.disclosure
 
org.intermine.web.tags.table - package org.intermine.web.tags.table
 
org.intermine.web.tags.util - package org.intermine.web.tags.util
 
org.intermine.web.task - package org.intermine.web.task
 
org.intermine.web.util - package org.intermine.web.util
 
org.intermine.webservice.client.core - package org.intermine.webservice.client.core
 
org.intermine.webservice.client.exceptions - package org.intermine.webservice.client.exceptions
 
org.intermine.webservice.client.lists - package org.intermine.webservice.client.lists
 
org.intermine.webservice.client.results - package org.intermine.webservice.client.results
 
org.intermine.webservice.client.services - package org.intermine.webservice.client.services
Contains all InterMine web services at one place.
org.intermine.webservice.client.template - package org.intermine.webservice.client.template
 
org.intermine.webservice.client.util - package org.intermine.webservice.client.util
 
org.intermine.webservice.client.widget - package org.intermine.webservice.client.widget
 
org.intermine.webservice.server - package org.intermine.webservice.server
Intermine and mines derived from Intermine implement RESTfull web services.
org.intermine.webservice.server.branding - package org.intermine.webservice.server.branding
 
org.intermine.webservice.server.clob - package org.intermine.webservice.server.clob
 
org.intermine.webservice.server.complexes - package org.intermine.webservice.server.complexes
 
org.intermine.webservice.server.core - package org.intermine.webservice.server.core
 
org.intermine.webservice.server.data - package org.intermine.webservice.server.data
 
org.intermine.webservice.server.exceptions - package org.intermine.webservice.server.exceptions
 
org.intermine.webservice.server.filter - package org.intermine.webservice.server.filter
 
org.intermine.webservice.server.idresolution - package org.intermine.webservice.server.idresolution
 
org.intermine.webservice.server.jbrowse - package org.intermine.webservice.server.jbrowse
 
org.intermine.webservice.server.jbrowse.genomic - package org.intermine.webservice.server.jbrowse.genomic
 
org.intermine.webservice.server.jbrowse.util - package org.intermine.webservice.server.jbrowse.util
 
org.intermine.webservice.server.lists - package org.intermine.webservice.server.lists
 
org.intermine.webservice.server.model - package org.intermine.webservice.server.model
 
org.intermine.webservice.server.output - package org.intermine.webservice.server.output
 
org.intermine.webservice.server.path - package org.intermine.webservice.server.path
 
org.intermine.webservice.server.query - package org.intermine.webservice.server.query
 
org.intermine.webservice.server.query.result - package org.intermine.webservice.server.query.result
 
org.intermine.webservice.server.search - package org.intermine.webservice.server.search
 
org.intermine.webservice.server.template - package org.intermine.webservice.server.template
 
org.intermine.webservice.server.template.result - package org.intermine.webservice.server.template.result
 
org.intermine.webservice.server.user - package org.intermine.webservice.server.user
 
org.intermine.webservice.server.widget - package org.intermine.webservice.server.widget
 
org.intermine.xml - package org.intermine.xml
 
org.intermine.xml.full - package org.intermine.xml.full
 
OrganismData - Class in org.intermine.bio.util
A class to hold data about one organism.
OrganismGenomeBuildLookup - Class in org.intermine.bio.web.logic
An util class to help looking up genome build by a given organism id.
OrganismInfo - Class in org.intermine.bio.web.model
Bean to store organism information for Galaxy use.
OrganismInfo(int, String, String) - Constructor for class org.intermine.bio.web.model.OrganismInfo
Constructor
OrganismRepository - Class in org.intermine.bio.util
A class to hold information about organisms.
organisms - Variable in class org.intermine.bio.dataconversion.UniprotFilterTask
 
organisms - Variable in class org.intermine.bio.postprocess.PostProcessOperationsTask
 
orgIdMainMaps - Variable in class org.intermine.bio.dataconversion.IdResolver
 
orgIdMaps - Variable in class org.intermine.bio.dataconversion.IdResolver
 
orgIdSynMaps - Variable in class org.intermine.bio.dataconversion.IdResolver
 
orgMainMaps - Variable in class org.intermine.bio.dataconversion.IdResolver
 
orgSynMaps - Variable in class org.intermine.bio.dataconversion.IdResolver
 
orgTaxonId - Variable in class org.intermine.bio.task.GFF3ConverterTask
 
origin - Variable in class org.intermine.api.search.OriginatingEvent
 
originalSql - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
OriginatingEvent - Class in org.intermine.api.search
A representation of a notification that something has happened that originated at a particular web searchable object.
OriginatingEvent(WebSearchable) - Constructor for class org.intermine.api.search.OriginatingEvent
Constructor.
originatingQuery - Variable in class org.intermine.api.results.ExportResultsIterator
 
OrthodbConverter - Class in org.intermine.bio.dataconversion
Orthodb data Converter
OrthodbConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.OrthodbConverter
Constructor
OrthologueConverter - Class in org.intermine.bio.web.logic
 
OrthologueConverter(InterMineAPI, WebConfig) - Constructor for class org.intermine.bio.web.logic.OrthologueConverter
 
os - Variable in class org.intermine.api.profile.ProfileManager
 
os - Variable in class org.intermine.api.query.QueryExecutor
 
os - Variable in class org.intermine.api.template.TemplateSummariser
 
os - Variable in class org.intermine.bio.postprocess.CalculateLocations
 
os - Variable in class org.intermine.bio.postprocess.EnsemblGwasDbPostprocess
 
os - Variable in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask
 
os - Variable in class org.intermine.bio.postprocess.GoPostprocess
 
os - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
os - Variable in class org.intermine.objectstore.ObjectStorePassthruImpl
 
os - Variable in class org.intermine.objectstore.query.ClobAccess
 
os - Variable in class org.intermine.objectstore.query.ResultsBatches
 
os - Variable in class org.intermine.objectstore.translating.Translator
 
os - Variable in class org.intermine.web.logic.widget.Widget
 
os - Variable in class org.intermine.web.logic.widget.WidgetLdr
 
os - Variable in class org.intermine.web.task.CreateSearchIndexTask
 
os - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
OS_FORMAT_VERSION - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key used to store objectstore format version number.
OS_SUMMARY - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key to use to store the objectstoresummary.properties file.
osAlias - Variable in class org.intermine.web.task.CreateSearchIndexTask
 
osb - Variable in class org.intermine.objectstore.query.BagConstraint
 
osName - Variable in class org.intermine.task.PostProcessorTask
 
osname - Variable in class org.intermine.task.RetrieveMetadataTask
 
osName - Variable in class org.intermine.task.StoreMetadataTask
 
oss - Variable in class org.intermine.api.InterMineAPI
 
osw - Variable in class org.intermine.api.template.TemplateSummariser
 
osw - Variable in class org.intermine.api.tracker.TrackerDelegate
 
osw - Variable in class org.intermine.api.tracker.xml.TrackHandler
 
osw - Variable in class org.intermine.bio.postprocess.CalculateLocations
 
osw - Variable in class org.intermine.bio.postprocess.CreateLocationOverlapIndex
 
osw - Variable in class org.intermine.bio.postprocess.CreateReferences
 
osw - Variable in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask
 
osw - Variable in class org.intermine.bio.postprocess.OverlapViewTask
 
osw - Variable in class org.intermine.bio.postprocess.PopulateChildFeatures
 
osw - Variable in class org.intermine.bio.postprocess.PostProcessOperationsTask
 
osw - Variable in class org.intermine.bio.postprocess.TransferSequences
 
osw - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
osw - Variable in class org.intermine.postprocess.PostProcessor
 
osWriter - Variable in class org.intermine.api.profile.TagManager
 
OTHER - Static variable in class org.intermine.api.bag.BagQueryResult
Key of the Map returned by getIssues() when the input string
OtherMinesLinkController - Class in org.intermine.bio.web
Show Other Mines Links on "Gene" page
OtherMinesLinkController() - Constructor for class org.intermine.bio.web.OtherMinesLinkController
 
OuterJoinStatus - Enum in org.intermine.pathquery
Enumeration for outer join status.
Output - Class in org.intermine.webservice.server.output
Abstract class representing an output of a web service.
Output() - Constructor for class org.intermine.webservice.server.output.Output
 
output - Variable in class org.intermine.webservice.server.WebService
The response to the outside world.
OUTPUT_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Name of format parameter that specifies format of returned results.
outputFile - Variable in class org.intermine.bio.postprocess.PostProcessOperationsTask
 
outputFile - Variable in class org.intermine.task.SummariseObjectStoreTask
 
outputModelFile - Variable in class org.intermine.task.ModelMergerTask
 
OUTSIDE - Static variable in class org.intermine.metadata.ConstraintOp
Require that some part of the first argument lie outside the second.
overlap(CalculateLocations.SimpleLoc, CalculateLocations.SimpleLoc) - Static method in class org.intermine.bio.postprocess.CalculateLocations
Return true if locations of two objects on some parent object have any overlap.
OverlapConstraint - Class in org.intermine.objectstore.query
Represents a constraint comparing two range values on an object.
OverlapConstraint(OverlapRange, ConstraintOp, OverlapRange) - Constructor for class org.intermine.objectstore.query.OverlapConstraint
Construct a constraint.
overlapConstraintToString(SqlGenerator.State, StringBuffer, OverlapConstraint, Query, DatabaseSchema, int) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts an OverlapConstraint to a String suitable for putting in an SQL query.
OverlappingFeaturesDisplayer - Class in org.intermine.bio.web.displayer
Displayer for features overlapping a particular SequenceFeature using the overlappingFeatures collection.
OverlappingFeaturesDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.OverlappingFeaturesDisplayer
Construct with config and the InterMineAPI.
OverlapRange - Class in org.intermine.objectstore.query
Represents a range value on an object.
OverlapRange(QueryEvaluable, QueryEvaluable, QueryObjectReference) - Constructor for class org.intermine.objectstore.query.OverlapRange
Constructor for this object.
OVERLAPS - Static variable in class org.intermine.metadata.ConstraintOp
Require that a range overlaps another range
OverlapUtil - Class in org.intermine.bio.postprocess
Utility methods for finding overlaps.
OverlapViewTask - Class in org.intermine.bio.postprocess
A task the replace the sequencefeatureoverlappingfeatures table with a view that uses the bioseg type to calculate the overlaps.
OverlapViewTask(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.OverlapViewTask
Construct a new OverlapViewTask that will change the given object store.

P

packageName(String) - Static method in class org.intermine.metadata.TypeUtil
Returns the package name from a fully qualified class name
packageName - Variable in class org.intermine.task.InheritanceDotTask
 
Page - Class in org.intermine.webservice.client.results
Object representing a page parameter.
Page(int, int) - Constructor for class org.intermine.webservice.client.results.Page
Construct a new page, specifying a start point and a size.
Page(int) - Constructor for class org.intermine.webservice.client.results.Page
Construct a new page, specifying a start point.
Page - Class in org.intermine.webservice.server.core
Parameter class for passing start and limit arguments to iterators.
Page(int, Integer) - Constructor for class org.intermine.webservice.server.core.Page
Construct a new page.
Page(int) - Constructor for class org.intermine.webservice.server.core.Page
Construct a new page, going from a certain row to the end of the result set.
PagedTable - Class in org.intermine.web.logic.results
Deprecated.
Use web-services instead.
PagedTable(WebTable) - Constructor for class org.intermine.web.logic.results.PagedTable
Deprecated.
Construct a PagedTable with a list of column names
PagedTable(WebTable, int) - Constructor for class org.intermine.web.logic.results.PagedTable
Deprecated.
Construct a PagedTable with a list of column names
pageName - Variable in class org.intermine.web.struts.ModifyBagForm
 
pageName - Variable in class org.intermine.web.struts.ModifyTemplateForm
 
PageOutOfRangeException - Exception in org.intermine.web.logic.results
PageOutOfRangeException class
PageOutOfRangeException(String, Throwable) - Constructor for exception org.intermine.web.logic.results.PageOutOfRangeException
Create a new PageOutOfRangeException.
PageOutOfRangeException(String) - Constructor for exception org.intermine.web.logic.results.PageOutOfRangeException
Create a new PageOutOfRangeException.
pageSize - Variable in class org.intermine.web.struts.ChangeTableSizeForm
 
PageTableQueryMonitor - Class in org.intermine.web.logic.query
An implementation of QueryMonitor that maintains a timeout and remembers which PagedTable it is monitoring
PageTableQueryMonitor(int, PagedTable) - Constructor for class org.intermine.web.logic.query.PageTableQueryMonitor
Construct a new instance of QueryMonitorTimeout.
Pair<A,B> - Class in org.intermine.webservice.server.core
A tuple of order two.
Pair(A, B) - Constructor for class org.intermine.webservice.server.core.Pair
Construct a pair of two things
PantherConverter - Class in org.intermine.bio.dataconversion
 
PantherConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.PantherConverter
Constructor
parallel - Variable in class org.intermine.sql.Database
The number of worker threads to use for background SQL statements
ParallelBatchingFetcher - Class in org.intermine.dataloader
Class providing EquivalentObjectFetcher functionality that fetches batches of equivalent objects in parallel to improve performance.
ParallelBatchingFetcher(BaseEquivalentObjectFetcher, DataTracker, Source) - Constructor for class org.intermine.dataloader.ParallelBatchingFetcher
Constructor
ParallelPrecomputer - Class in org.intermine.objectstore.intermine
An object that can perform a set of precomputes in parallel.
ParallelPrecomputer(ObjectStoreInterMineImpl, int) - Constructor for class org.intermine.objectstore.intermine.ParallelPrecomputer
Constructor.
ParallelPrecomputer.Job - Class in org.intermine.objectstore.intermine
Class representing a precomputing job to be performed.
ParallelPrecomputer.Job(String, Query, Collection<? extends QueryNode>, boolean, String) - Constructor for class org.intermine.objectstore.intermine.ParallelPrecomputer.Job
Constructor - takes the same arguments as ObjectStoreInterMineImpl.precompute().
parameterIsRequired(String) - Method in class org.intermine.webservice.server.widget.WidgetsRequestParser
Declare that a particular parameter is required.
params - Variable in class org.intermine.web.struts.ForwardParameters
Map from parameter name to parameter value.
parent - Variable in class org.intermine.objectstore.query.OverlapRange
 
parents - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler
 
parse(BufferedReader) - Method in class org.intermine.bio.dataconversion.GFF3Converter
Parse a bufferedReader and process GFF3 record
parse(BufferedReader) - Static method in class org.intermine.bio.io.gff3.GFF3Parser
Read GFF3 lines from a BufferedReader and return an Iterator over the GFF3Records.
parse(InputSource, DefaultHandler) - Static method in class org.intermine.metadata.SAXParser
Parse the an xml file
parse(InputSource, DefaultHandler, boolean) - Static method in class org.intermine.metadata.SAXParser
Parse the an xml file
parse(String, ObjectStoreInterMineImpl) - Static method in class org.intermine.objectstore.intermine.NotXmlParser
Parse the given NotXml String into an Object.
parse(IqlQuery) - Static method in class org.intermine.objectstore.query.iql.IqlQueryParser
Construct a new query by parsing a String.
parse(String, Class<?>) - Static method in class org.intermine.pathquery.ConstraintValueParser
Parses a value.
parse(InputSource, DefaultHandler) - Static method in class org.intermine.util.SAXParser
Parse the an xml file
parse(InputSource, DefaultHandler, boolean) - Static method in class org.intermine.util.SAXParser
Parse the an xml file
parse(ServletContext, Model) - Static method in class org.intermine.web.logic.config.WebConfig
Parse a WebConfig XML file
parse(ResultsRow<?>) - Method in interface org.intermine.webservice.server.core.ResultRowParser
Parse result row to list of strings.
parse(InputStream) - Static method in class org.intermine.xml.full.FullParser
Parse a InterMine Full XML file
parseBasicInput(GenomicRegionSearchForm) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
 
parseConstraints(HttpServletRequest) - Static method in class org.intermine.web.logic.template.Templates
Given a HTTP request, parse out the template values.
parseCsvDelimitedReader(Reader) - Static method in class org.intermine.util.FormattedTextParser
Return an Iterator over a comma/tab delimited file.
parseDelimitedReader(Reader, char) - Static method in class org.intermine.util.FormattedTextParser
Return an Iterator over a delimited file.
parseError(String) - Static method in class org.intermine.webservice.client.util.ErrorMessageParser
Parses service error message.
parseExtension(String) - Static method in class org.intermine.bio.webservice.FastaQueryService
A method for parsing the value of the extension parameter.
parseFacets(BrowseResult, Vector<KeywordSearchFacetData>, Map<String, String>) - Static method in class org.intermine.api.lucene.KeywordSearch
 
parseFileNames(File[]) - Method in class org.intermine.bio.dataconversion.UniprotConverter
sprot data files need to be processed immediately before trembl ones not all organisms are going to have both files UniProtFilterTask has already been run so all files are assumed to be valid.
parseFormatFromPathInfo(HttpServletRequest) - Static method in class org.intermine.webservice.server.WebServiceRequestParser
Parse a format from the path-info of the request.
parseGenomicRegionSearchForm(GenomicRegionSearchForm) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
To parse form data
parseList(ServiceFactory, JSONObject) - Static method in class org.intermine.webservice.client.lists.Lists
Parse a list from its representation in JSON.
parseListCreationInfo(ServiceFactory, String) - Static method in class org.intermine.webservice.client.lists.Lists
Construct a representation of a list from the data returned by a call to create a new list.
parseParameterMap(String) - Static method in class org.intermine.webservice.client.util.URLParser
Returns parameters of URL as parameter map where key in the map is the parameter name and value is list of parameter values.
parser - Variable in class org.intermine.bio.task.GFF3ConverterTask
 
parseRange(String) - Method in class org.intermine.api.query.range.AbstractHelper
Construct a Range object from a string defining one of the ranges this constraint operates on.
parseRange(String) - Method in class org.intermine.model.testmodel.query.range.EmploymentPeriodHelper
 
parseRegion(String, boolean, Map<String, ChromosomeInfo>) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchUtil
Parse region from string to GenomicRegion object
parseRequest(HttpServletRequest, WebServiceInput) - Method in class org.intermine.webservice.server.WebServiceRequestParser
Parses common parameters for all web services.
parseResults(InterMineAPI, WebConfig, Collection<KeywordSearchHit>) - Static method in class org.intermine.web.search.SearchUtils
Parse the results into a human friendly form
parseServiceUrl(String) - Static method in class org.intermine.webservice.client.util.URLParser
Returns service URL - i.e.
parseTabDelimitedReader(Reader) - Static method in class org.intermine.util.FormattedTextParser
Return an Iterator over a tab delimited file.
parseValue(String, Class<?>, ActionMessages) - Static method in class org.intermine.web.struts.QueryBuilderConstraintForm
Parse an attribute value
ParseValueException - Exception in org.intermine.pathquery
Exception thrown during parsing constraint value.
ParseValueException(String) - Constructor for exception org.intermine.pathquery.ParseValueException
Constructor
ParseValueException(String, Throwable) - Constructor for exception org.intermine.pathquery.ParseValueException
Constructor.
participant - Variable in class org.intermine.webservice.server.complexes.ExportService.FeatureHolder
 
PartnerLink - Class in org.intermine.api.beans
A bean that contains the information to define a matching set of objects.
PartnerLink() - Constructor for class org.intermine.api.beans.PartnerLink
 
PartnerLinkBeanInfo - Class in org.intermine.api.beans
An object that describes the PartnerLink bean and supports DWR serialization.
PartnerLinkBeanInfo() - Constructor for class org.intermine.api.beans.PartnerLinkBeanInfo
 
password - Variable in class org.intermine.api.profile.Profile
 
password - Variable in class org.intermine.web.struts.CreateAccountForm
 
password - Variable in class org.intermine.web.struts.LoginForm
 
password - Variable in class org.intermine.web.struts.RequestPasswordForm
 
password2 - Variable in class org.intermine.web.struts.CreateAccountForm
 
PasswordHasher - Class in org.intermine.util
Utility methods for managing hashed passwords
PasswordResetAction - Class in org.intermine.web.struts
Action to change a user's password with the authority of a token previously emailed to them.
PasswordResetAction() - Constructor for class org.intermine.web.struts.PasswordResetAction
 
PasswordResetController - Class in org.intermine.web.struts
Controller for the password reset page.
PasswordResetController() - Constructor for class org.intermine.web.struts.PasswordResetController
 
PasswordResetForm - Class in org.intermine.web.struts
The form for resetting a password.
PasswordResetForm() - Constructor for class org.intermine.web.struts.PasswordResetForm
 
Path - Class in org.intermine.pathquery
Object to represent a path through an InterMine model.
Path(Model, String) - Constructor for class org.intermine.pathquery.Path
Create a new Path object.
Path(Model, String, Map<String, String>) - Constructor for class org.intermine.pathquery.Path
Create a Path object using class constraints from a Map.
path - Variable in class org.intermine.pathquery.PathConstraint
 
path - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
PATH_BAG_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
PathConstraint - Class in org.intermine.pathquery
Representation of a constraint in the PathQuery.
PathConstraint(String, ConstraintOp) - Constructor for class org.intermine.pathquery.PathConstraint
Constructs a new PathConstraint.
PathConstraintAttribute - Class in org.intermine.pathquery
Representation of a normal attribute constraint in the PathQuery
PathConstraintAttribute(String, ConstraintOp, String) - Constructor for class org.intermine.pathquery.PathConstraintAttribute
Constructs a new PathConstraintAttribute.
PathConstraintBag - Class in org.intermine.pathquery
Representation of a constraint to a bag in the PathQuery
PathConstraintBag(String, ConstraintOp, String) - Constructor for class org.intermine.pathquery.PathConstraintBag
Constructs a new PathConstraintBag.
PathConstraintIds - Class in org.intermine.pathquery
Representation of a constraint to a collection of object ids in a query.
PathConstraintIds(String, ConstraintOp, Collection<Integer>) - Constructor for class org.intermine.pathquery.PathConstraintIds
Constructs a new PathConstraintIds.
PathConstraintLookup - Class in org.intermine.pathquery
Representation of a lookup constraint in the PathQuery
PathConstraintLookup(String, String, String) - Constructor for class org.intermine.pathquery.PathConstraintLookup
Constructs a new PathConstraintLookup.
PathConstraintLoop - Class in org.intermine.pathquery
Representation of a loop constraint in the PathQuery
PathConstraintLoop(String, ConstraintOp, String) - Constructor for class org.intermine.pathquery.PathConstraintLoop
Constructs a new PathConstraintLoop from one path to another.
PathConstraintMultitype - Class in org.intermine.pathquery
A constraint that restricts a path to inhabiting one of a list of types.
PathConstraintMultitype(String, ConstraintOp, Collection<String>) - Constructor for class org.intermine.pathquery.PathConstraintMultitype
Construct a multi-type constraint.
PathConstraintMultiValue - Class in org.intermine.pathquery
Representation of a constraint to a collection of values in a query.
PathConstraintMultiValue(String, ConstraintOp, Collection<String>) - Constructor for class org.intermine.pathquery.PathConstraintMultiValue
Constructs a new PathConstraintMultiValue.
PathConstraintNull - Class in org.intermine.pathquery
Representation of a null attribute constraint in the PathQuery
PathConstraintNull(String, ConstraintOp) - Constructor for class org.intermine.pathquery.PathConstraintNull
Constructs a new PathConstraintNull.
PathConstraintRange - Class in org.intermine.pathquery
A constraint that restrict a path to a particular relationship with a set of ranges.
PathConstraintRange(String, ConstraintOp, Collection<String>) - Constructor for class org.intermine.pathquery.PathConstraintRange
Constructs a new PathConstraintRange.
PathConstraintSubclass - Class in org.intermine.pathquery
Representation of a subclass constraint in the PathQuery.
PathConstraintSubclass(String, String) - Constructor for class org.intermine.pathquery.PathConstraintSubclass
Constructs a new PathConstraintSubclass.
PathException - Exception in org.intermine.pathquery
An Exception thrown if there is a problem in the Path class.
PathException(String, String) - Constructor for exception org.intermine.pathquery.PathException
Create a new PathException with the given message.
PathExpressionField - Class in org.intermine.objectstore.query
An element that can appear in the SELECT clause of a query, representing extra data to be collected for the Results - namely a part of the SELECT list of a QueryObjectPathExpression in single-row mode.
PathExpressionField(QueryObjectPathExpression, int) - Constructor for class org.intermine.objectstore.query.PathExpressionField
Constructor.
PathLengthComparator - Class in org.intermine.pathquery
 
PathLengthComparator() - Constructor for class org.intermine.pathquery.PathLengthComparator
protected constructor
pathQuery - Variable in class org.intermine.api.profile.PathQueryUpdate
 
PathQuery - Class in org.intermine.pathquery
Class to represent a path-based query.
PathQuery(Model) - Constructor for class org.intermine.pathquery.PathQuery
Constructor.
PathQuery(PathQuery) - Constructor for class org.intermine.pathquery.PathQuery
Constructor.
PathQueryAPI - Class in org.intermine.api.query
Provides methods to obtain PathQueryExecutors and WebResultsExecutors
PathQueryBinding - Class in org.intermine.pathquery
Convert PathQueries to and from XML
PathQueryBinding() - Constructor for class org.intermine.pathquery.PathQueryBinding
 
PathQueryBuilder - Class in org.intermine.webservice.server.query.result
PathQueryBuilder builds PathQuery object from xml and validates it.
PathQueryBuilder(String, String, Producer<Map<String, InterMineBag>>) - Constructor for class org.intermine.webservice.server.query.result.PathQueryBuilder
PathQueryBuilder constructor.
PathQueryBuilderForJSONObj - Class in org.intermine.webservice.server.query.result
 
PathQueryBuilderForJSONObj() - Constructor for class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj
Constructor.
PathQueryBuilderForJSONObj(String, String, Producer<Map<String, InterMineBag>>) - Constructor for class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj
Constructor
PathQueryExecutor - Class in org.intermine.api.query
Executes path query and returns results in form suitable for export or web services.
PathQueryExecutor(ObjectStore, Profile, BagQueryRunner, BagManager) - Constructor for class org.intermine.api.query.PathQueryExecutor
Constructor with necessary objects.
pathQueryFormat - Variable in class org.intermine.api.profile.ProfileManager
Number determining format of queries in the database
PathQueryHandler - Class in org.intermine.pathquery
Extension of DefaultHandler to handle parsing PathQuery objects
PathQueryHandler(Map<String, PathQuery>, int) - Constructor for class org.intermine.pathquery.PathQueryHandler
Constructor
PathQueryHandler(Map<String, PathQuery>, int, Model) - Constructor for class org.intermine.pathquery.PathQueryHandler
Constructor.
pathQueryIsPublic(PathQuery, InterMineAPI, Profile) - Static method in class org.intermine.web.struts.WebserviceCodeGenAction
Utility function to determine whether the PathQuery is publicly accessible.
pathQueryIsPublic(PathQuery, InterMineAPI, Profile) - Static method in class org.intermine.webservice.server.query.CodeService
Utility function to determine whether the PathQuery is publicly accessible.
PathQueryResultHelper - Class in org.intermine.web.logic.pathqueryresult
Helper for everything related to PathQueryResults
pathQueryToOSQ(PathQuery) - Static method in class org.intermine.webservice.server.jbrowse.Queries
For making queries that will not require LOOKUP constraints.
pathQueryToOSQ(PathQuery, BagQueryRunner) - Static method in class org.intermine.webservice.server.jbrowse.Queries
For making queries that will or might require LOOKUP constraints.
PathQueryUpdate - Class in org.intermine.api.profile
Class for updating a pathquery with a new model
PathQueryUpdate() - Constructor for class org.intermine.api.profile.PathQueryUpdate
Default constructor
PathQueryUpdate(PathQuery, Model) - Constructor for class org.intermine.api.profile.PathQueryUpdate
Construct with pathquery and former model
pathToIndex - Variable in class org.intermine.api.results.WebResults
 
PathUtil - Class in org.intermine.api.util
Utility methods for Paths
PathwayDescriptionDisplayer - Class in org.intermine.bio.web.displayer
 
PathwayDescriptionDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.PathwayDescriptionDisplayer
 
pathwayIdentifiers - Variable in class org.intermine.bio.dataconversion.KeggPathwayConverter
 
PathwaysDisplayer - Class in org.intermine.bio.web.displayer
Display pathway for this gene, plus the count of the other genes on this pathway
PathwaysDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.PathwaysDisplayer
Construct with config and the InterMineAPI.
pathwaysNotStored - Variable in class org.intermine.bio.dataconversion.KeggPathwayConverter
 
pathWithNoConstraints(String) - Method in class org.intermine.web.logic.widget.TableWidgetLdr
 
PdbConverter - Class in org.intermine.bio.dataconversion
 
PdbConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.PdbConverter
Create a new PdbConverter object.
pending - Static variable in class org.intermine.objectstore.query.PrefetchManager
Pending set of requests - always accessed inside a synchronise on sync.
PendingClob - Class in org.intermine.objectstore.query
Subclass of ClobAccess that contains data to be written to the database instead of access to data already in the database.
PendingClob(String) - Constructor for class org.intermine.objectstore.query.PendingClob
Construct a PendingClob from a String.
PER_PAGE - Static variable in class org.intermine.api.lucene.KeywordSearch
maximum number of items to be displayed on a page
PerformanceTester - Class in org.intermine.web.commandline
Class to run a performance test on a production database by loading a set of template queries from a userprofile database and running them in varying numbers of threads.
performSearch(String, String) - Method in class org.intermine.web.autocompletion.LuceneSearchEngine
Perform the lucene search.
performUnsafeOperation(String, SQLOperation<T>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Convenience wrapper to manage the boilerplate when performing unsafe operations.
perm - Variable in class org.intermine.task.GrantTask
 
PermaTokenDeletionService - Class in org.intermine.webservice.server.user
Does what it says on the tin.
PermaTokenDeletionService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.user.PermaTokenDeletionService
Constructor.
PermaTokenInfoService - Class in org.intermine.webservice.server.user
 
PermaTokenInfoService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.user.PermaTokenInfoService
 
PermaTokens - Class in org.intermine.webservice.server.user
 
PermaTokensServlet - Class in org.intermine.webservice.server.user
 
PermaTokensServlet() - Constructor for class org.intermine.webservice.server.user.PermaTokensServlet
 
pilferObjectById(Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Gets a object from the cache if it is present.
pilferObjectById(Integer) - Method in interface org.intermine.objectstore.ObjectStore
Gets a object from the cache if it is present.
pilferObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Gets a object from the cache if it is present.
pilferObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Gets a object from the cache if it is present.
pkQueryFruitless(Class<? extends FastPathObject>, String, Object) - Method in class org.intermine.dataloader.EquivalentObjectHints
Returns true if there were no instances of the given class with the given field set to the given value.
PkQueryIdUpgrader - Class in org.intermine.web.bag
Bag object id upgrader that uses the primary keys to find the objects in the new ObjectStore.
PkQueryIdUpgrader(ObjectStore) - Constructor for class org.intermine.web.bag.PkQueryIdUpgrader
No argument constructor - will use all available keyDefs to upgrade bags.
PkQueryIdUpgrader(String, ObjectStore) - Constructor for class org.intermine.web.bag.PkQueryIdUpgrader
Construct with the name of a source - will use defined keys to upgrade bags.
PLAIN_TEXT - Static variable in class org.intermine.webservice.server.lists.ListUploadService
 
PlainFormatter - Class in org.intermine.webservice.server.output
Simplest possible formatting.
PlainFormatter() - Constructor for class org.intermine.webservice.server.output.PlainFormatter
 
platform - Variable in class org.intermine.sql.Database
 
pluralise(String) - Static method in class org.intermine.metadata.StringUtil
Returns a pluralised version of the given String
PLUS - Static variable in class org.intermine.sql.query.Function
PLUS function - takes two or more operands.
POLL_REFRESH_SECONDS - Static variable in class org.intermine.web.logic.Constants
Refresh period specified on query poll page.
PollQueryAction - Class in org.intermine.web.struts
Repeatedly poll the status of a running query and forward client to appropriate page each time.
PollQueryAction() - Constructor for class org.intermine.web.struts.PollQueryAction
 
popTag() - Method in class org.intermine.webservice.server.output.XMLFormatter
Say that we are finished with the current tag.
PopulateChildFeatures - Class in org.intermine.bio.postprocess
Populate the SequenceFeature.childFeatures() collection for: Gene, Transcript, Exon Only used for JBrowse
PopulateChildFeatures(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.PopulateChildFeatures
Construct with an ObjectStoreWriter, read and write from same ObjectStore
populateCollection() - Method in class org.intermine.bio.postprocess.PopulateChildFeatures
Populate the SequenceFeature.locatedFeatures() collection for: Gene, Transcript, Exon and CDS
populateFromFile(File) - Method in class org.intermine.bio.dataconversion.IdResolver
Read contents of an IdResolver from file, allows for caching during a build.
populateIds(Connection, InterMineObject) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Populates the object o with IDs.
populateList(List<String>, String) - Method in class org.intermine.webservice.server.lists.ListInput
read the parameters into a list.
populateListMap(Map<String, InterMineBag>, String) - Method in class org.intermine.webservice.server.lists.ListInput
Fill a map with intermine bags from the names in a parameter.
populateNormedList(List<String>, String) - Method in class org.intermine.webservice.server.lists.ListInput
Read parameters into a list, normalising the values.
populateObject(Item, Map<String, FastPathObject>, boolean, boolean, FastPathObject) - Static method in class org.intermine.xml.full.FullParser
Fill in fields of an outline business object which is in the map under item.identifier Note that this modifies the relevant object in the map It also returns the object for convenience
populateRequest(HttpServletRequest, HttpServletResponse) - Static method in class org.intermine.web.struts.QueryBuilderController
Populate the request with the necessary attributes to render the query builder page.
populateSearchItems() - Method in class org.intermine.api.search.GlobalRepository
 
populateSearchItems() - Method in class org.intermine.api.search.SearchRepository
Collect the search items we are interested in initially.
populateSearchItems() - Method in class org.intermine.api.search.UserRepository
 
populateSOTermMap(ObjectStore) - Method in class org.intermine.bio.postprocess.PopulateChildFeatures
 
populateTemplateOneConstraint(TemplateQuery, ConstraintOp, String) - Static method in class org.intermine.api.template.TemplatePopulator
Populate a TemplateQuery that has a single editable constraint with the given value.
populateTemplateWithBag(TemplateQuery, InterMineBag) - Static method in class org.intermine.api.template.TemplatePopulator
Constrain a template query with a single editable constraint to be in the given bag.
populateTemplateWithObject(TemplateQuery, InterMineObject) - Static method in class org.intermine.api.template.TemplatePopulator
Constrain a template query with a single editable constraint to be the given object.
populationBagName - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
PopulationInfo - Class in org.intermine.web.logic.widget
Container for size and extra attribute (e.g. gene length average) for the whole population
PopulationInfo(int, float) - Constructor for class org.intermine.web.logic.widget.PopulationInfo
Constructor
PORTAL_MSG - Static variable in class org.intermine.web.logic.Constants
Session attribute that temporarily holds messages from the Portal
PortalHelper - Class in org.intermine.web.logic
Util methods for the portal
PortalQueryAction - Class in org.intermine.web.struts
The portal query action handles links into flymine from external sites.
PortalQueryAction() - Constructor for class org.intermine.web.struts.PortalQueryAction
 
possibleValues - Variable in class org.intermine.api.template.TemplateSummariser
 
PossibleValuesService - Class in org.intermine.webservice.server.path
A service for retrieving the possible values for a path in the data model.
PossibleValuesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.path.PossibleValuesService
A service for providing column summary information.
PossibleValuesServlet - Class in org.intermine.webservice.server.path
A servlet for routing requests to the possible values service.
PossibleValuesServlet() - Constructor for class org.intermine.webservice.server.path.PossibleValuesServlet
Constructor.
postDeleteBatch - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
PostgresByteArrayOutputStream - Class in org.intermine.sql.writebatch
A subclass of SensibleByteArrayOutputStream that has extra methods useful for reducing the memory footprint of the Postgres database write operations.
PostgresByteArrayOutputStream() - Constructor for class org.intermine.sql.writebatch.PostgresByteArrayOutputStream
 
PostgresByteArrayOutputStream(int) - Constructor for class org.intermine.sql.writebatch.PostgresByteArrayOutputStream
 
PostgresDataOutputStream - Class in org.intermine.sql.writebatch
A subclass of DataOutputStream that has extra methods useful for reducing the memory footprint of the Postgres database write operations.
PostgresDataOutputStream(OutputStream) - Constructor for class org.intermine.sql.writebatch.PostgresDataOutputStream
 
PostgresExplainResult - Class in org.intermine.sql.query
Subclass of ExplainResult specific to PostgreSQL.
PostgresExplainResult() - Constructor for class org.intermine.sql.query.PostgresExplainResult
Constructs an instance of PostgresExplainResult without any data.
PostgresExplainResult(Query, Connection) - Constructor for class org.intermine.sql.query.PostgresExplainResult
Constructs an instance of PostgresExplainResult for a given Query and database Connection.
PostgresExplainResult(String, Connection) - Constructor for class org.intermine.sql.query.PostgresExplainResult
Constructs an instance of PostgresExplainResult for a given Query String and database Connection.
PostgresExplainResult(PreparedStatement) - Constructor for class org.intermine.sql.query.PostgresExplainResult
Constructs an instance of ExplainResult given a PreparedStatement object.
postInit() - Method in class org.intermine.webservice.server.core.JSONService
 
postInit() - Method in class org.intermine.webservice.server.lists.ListShareDetailsService
 
postInit() - Method in class org.intermine.webservice.server.path.PossibleValuesService
 
postInit() - Method in class org.intermine.webservice.server.query.QueryRetrieverService
 
postInit() - Method in class org.intermine.webservice.server.query.QueryUploadService
 
postInit() - Method in class org.intermine.webservice.server.query.result.QueryResultService
 
postInit() - Method in class org.intermine.webservice.server.WebService
Subclasses can hook in here to do common behaviour that needs to happen after initialisation.
postProcess() - Method in class org.intermine.bio.postprocess.EnsemblGwasDbPostprocess
Set names and firstAuthors on GWAS objects from the referenced publication.
postProcess() - Method in class org.intermine.bio.postprocess.FlyBasePostProcess
All subclasses should override this method so they can be called in a generic fashion.
postProcess() - Method in class org.intermine.bio.postprocess.GoPostprocess
Copy all GO annotations from the Protein objects to the corresponding Gene(s)
postProcess() - Method in class org.intermine.bio.postprocess.ReactomePostProcess
All subclasses should override this method so they can be called in a generic fashion.
postProcess() - Method in class org.intermine.postprocess.PostProcessor
All subclasses should override this method so they can be called in a generic fashion.
PostProcess - Class in org.intermine.task.project
A representation of a post-processing production step.
PostProcess() - Constructor for class org.intermine.task.project.PostProcess
 
PostProcessOperationsTask - Class in org.intermine.bio.postprocess
Run operations on genomic model database after DataLoading
PostProcessOperationsTask() - Constructor for class org.intermine.bio.postprocess.PostProcessOperationsTask
 
PostProcessor - Class in org.intermine.postprocess
Generic defn of a post process step...
PostProcessor(ObjectStoreWriter) - Constructor for class org.intermine.postprocess.PostProcessor
Typical constructor with a handle to the object store we are working on.
POSTPROCESSOR_CLASS - Static variable in class org.intermine.task.PostProcessTask
The property (from "project.properties") that sets the postprocessor class to use.
PostProcessorTask - Class in org.intermine.task
Generic defn of a post process step...
PostProcessorTask() - Constructor for class org.intermine.task.PostProcessorTask
 
PostProcessTask - Class in org.intermine.task
Class that operates on the PostProcessing section of a Mines project.xml file.
PostProcessTask() - Constructor for class org.intermine.task.PostProcessTask
 
PostProcessUtil - Class in org.intermine.bio.postprocess
Common operations for post processing.
POWER - Static variable in class org.intermine.sql.query.Function
POWER function - takes two operands.
PQUtil - Class in org.intermine.webservice.client.util
Static methods to make certain path-query based operations easier.
preCompute(String) - Method in class org.intermine.dwr.AjaxServices
Precomputes the given template query
precompute(Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates precomputed tables for the given query.
precompute(Query, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates precomputed tables for the given query.
precompute(Query, Collection<? extends QueryNode>, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates precomputed tables for the given query.
precompute(Query, Collection<? extends QueryNode>, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates precomputed tables for the given query.
precompute(Collection<ParallelPrecomputer.Job>) - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer
Perform a load of precompute operations in parallel.
precompute(boolean, ObjectStore, int) - Method in class org.intermine.task.PrecomputeTask
Create precomputed tables for the given ObjectStore.
precompute(Query, Collection<QueryNode>, String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Call ObjectStoreInterMineImpl.precompute() with the given Query.
PRECOMPUTE_CATEGORY - Static variable in class org.intermine.bio.util.Constants
The category to pass to ObjectStoreInterMineImpl.precompute().
PRECOMPUTE_CATEGORY_TEMPLATE - Static variable in class org.intermine.web.task.PrecomputeTemplatesTask
The precompute category to use for templates.
PrecomputedTable - Class in org.intermine.sql.precompute
Represents a Precomputed table in a database.
PrecomputedTable(Query, String, String, String, Connection) - Constructor for class org.intermine.sql.precompute.PrecomputedTable
Construct a new PrecomputedTable
PrecomputedTableManager - Class in org.intermine.sql.precompute
Manages all the Precomputed tables in a given database.
PrecomputedTableManager(Connection) - Constructor for class org.intermine.sql.precompute.PrecomputedTableManager
Create a PrecomputedTableManager for a given Connection.
PrecomputedTableManager(Database) - Constructor for class org.intermine.sql.precompute.PrecomputedTableManager
Create a PrecomputedTableManager for the given underlying database.
precomputedTables - Variable in class org.intermine.sql.precompute.PrecomputedTableManager
 
precomputeQuery(String, Query, Collection<? extends QueryNode>, boolean, String, int) - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer
Call ObjectStoreInterMineImpl.precompute() with the given Query.
PrecomputeTask - Class in org.intermine.task
A Task that reads a list of queries from a properties file (eg. testmodel_precompute.properties) and calls ObjectStoreInterMineImpl.precompute() using the Query.
PrecomputeTask() - Constructor for class org.intermine.task.PrecomputeTask
 
precomputeTemplate(TemplateQuery) - Method in class org.intermine.api.query.WebResultsExecutor
Precomputes a template query if it is not already precomputed, returning whether precomputing was necessary.
precomputeTemplates() - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Create precomputed tables for all template queries in the given ObjectStore.
PrecomputeTemplatesTask - Class in org.intermine.web.task
A Task that reads a list of queries from a properties file (eg. testmodel_precompute.properties) and calls ObjectStoreInterMineImpl.precompute() using the Query.
PrecomputeTemplatesTask() - Constructor for class org.intermine.web.task.PrecomputeTemplatesTask
 
precomputeWithConnection(Connection, Query, Collection<? extends QueryNode>, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates precomputed tables with the given query and connection.
preDeleteBatch - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
Predicate<T> - Interface in org.intermine.webservice.server.core
The type of functions that test things.
PreferencesHandler - Class in org.intermine.api.profile
 
PreferencesHandler(Map<String, String>) - Constructor for class org.intermine.api.profile.PreferencesHandler
 
PreferencesManager - Class in org.intermine.api.profile
Class encapsulating the logic for reading user preferences in and out of the DB.
PreferencesManager(ObjectStoreWriter) - Constructor for class org.intermine.api.profile.PreferencesManager
Constructor
prefers(String) - Method in class org.intermine.api.profile.Profile
Determine whether a user perfers a certain thing or not.
prefetch - Variable in class org.intermine.objectstore.query.Results
 
prefetch(int, boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches
Prefetch into memory the batch indicated with the given batch number.
prefetchIds(Set<Integer>) - Method in class org.intermine.dataloader.DataTracker
Prefetches data for a specified set of object ids.
PrefetchManager - Class in org.intermine.objectstore.query
A manager for the prefetch mechanism for the Results object.
prefetchObjectById(Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Prefetches an object into the objectstore getObjectById cache.
prefetchObjectById(Integer) - Method in interface org.intermine.objectstore.ObjectStore
Prefetches an object into the objectstore getObjectById cache.
prefetchObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Prefetches an object into the objectstore getObjectById cache.
prefetchObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Prefetches an object into the objectstore getObjectById cache.
prefix - Variable in class org.intermine.bio.dataconversion.OboConverter
 
prettyList(Collection<String>) - Static method in class org.intermine.metadata.StringUtil
Take a collection of Strings and return a combined string as a comma separated list with 'and' between the final pair.
prettyList(Collection<String>, boolean) - Static method in class org.intermine.metadata.StringUtil
Take a collection of Strings and return a combined string as a comma separated list with 'and' between the final pair.
PREV_TEMPLATE_NAME - Static variable in class org.intermine.web.logic.Constants
Session attribute used to store the previous template name
previousPage() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Go to the previous page
primaryIdentifier - Variable in class org.intermine.webservice.server.complexes.ExportService.FeatureHolder
 
PrimaryKey - Class in org.intermine.metadata
Class representing a primary key as a list of field names
PrimaryKey(String, String, ClassDescriptor) - Constructor for class org.intermine.metadata.PrimaryKey
Constructor
primaryKeyCache - Static variable in class org.intermine.metadata.PrimaryKeyUtil
 
PrimaryKeyUtil - Class in org.intermine.metadata
Utility methods for PrimaryKey objects.
println() - Method in class org.intermine.web.logic.export.CustomPrintWriter
printStyleAndClass(JspWriter) - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
Prints 'style' and 'class' attributes of element.
priorityConfig - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
 
PriorityConfig - Class in org.intermine.dataloader
Class holding data source priority configuration for a Model.
PriorityConfig(Model) - Constructor for class org.intermine.dataloader.PriorityConfig
Constructor.
PRIVATEKEY_ALIAS - Static variable in class org.intermine.web.task.IssueTokenTask
The alias of the private key
PRIVATEKEY_PASSWORD - Static variable in class org.intermine.web.task.IssueTokenTask
The password of the private key.
process(Reader) - Method in class org.intermine.bio.dataconversion.BioGridConverter
Perform the currentFile conversion
process() - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
Process the data from the Database and write to the ItemWriter.
process(Connection) - Method in class org.intermine.bio.dataconversion.ChadoProcessor
Do the processing for this module - called by ChadoDBConverter.
process(Reader) - Method in class org.intermine.bio.dataconversion.EnsemblComparaConverter
Perform the currentFile conversion
process() - Method in class org.intermine.bio.dataconversion.EnsemblGwasDbConverter
Query from database and write items to the writer.
process() - Method in class org.intermine.bio.dataconversion.EnsemblSnpDbConverter
Query from database and write items to the writer.
process(ResultSet, String) - Method in class org.intermine.bio.dataconversion.EnsemblSnpDbConverter
process() - Method in class org.intermine.bio.dataconversion.EnsembSnpLoaderTask
Process and load the SNP file.
process() - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
Process and load all of the fasta files.
process(GFF3Record) - Method in class org.intermine.bio.dataconversion.GFF3Converter
process GFF3 record and give a xml presentation
process(GFF3Record) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Method to perform additional operations for a GFF3Record.
process(Reader) - Method in class org.intermine.bio.dataconversion.GoConverter
Perform the currentFile conversion
process(Reader) - Method in class org.intermine.bio.dataconversion.HomologeneConverter
Perform the currentFile conversion
process(Reader) - Method in class org.intermine.bio.dataconversion.InterProConverter
Perform the currentFile conversion
process(Reader) - Method in class org.intermine.bio.dataconversion.InterproGoConverter
Perform the currentFile conversion
process(Reader) - Method in class org.intermine.bio.dataconversion.KeggOrthologuesConverter
Perform the currentFile conversion
process(Reader) - Method in class org.intermine.bio.dataconversion.KeggPathwayConverter
Read each line from flat file, create genes and synonyms.
process(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
Do the processing for this module - called by ChadoDBConverter.
process(GFF3Record) - Method in class org.intermine.bio.dataconversion.NcbiGffGFF3RecordHandler
Method to perform additional operations for a GFF3Record.
process() - Method in class org.intermine.bio.dataconversion.OboConverter
Process every DAG term and output it as a Item.
process(OboTerm) - Method in class org.intermine.bio.dataconversion.OboConverter
Convert a OboTerm into an Item and relation Items, and write the relations to the writer.
process(Reader) - Method in class org.intermine.bio.dataconversion.OrthodbConverter
Perform the currentFile conversion
process(Reader) - Method in class org.intermine.bio.dataconversion.PantherConverter
Process the text file
process(File) - Method in class org.intermine.bio.dataconversion.PdbConverter
Perform the conversion files in the directory
process(Reader) - Method in class org.intermine.bio.dataconversion.Protein2iprConverter
Perform the currentFile conversion
process(Reader) - Method in class org.intermine.bio.dataconversion.PsiComplexesConverter
Perform the currentFile conversion
process(Reader) - Method in class org.intermine.bio.dataconversion.PsiConverter
Perform the currentFile conversion
process(Reader) - Method in class org.intermine.bio.dataconversion.PubMedGeneConverter
Process references file and gene information file.
process(Reader) - Method in class org.intermine.bio.dataconversion.ReactomeConverter
Perform the currentFile conversion
process(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Do the processing for this module - called by ChadoDBConverter.
process(Connection) - Method in class org.intermine.bio.dataconversion.StockProcessor
Do the processing for this module - called by ChadoDBConverter.
process(Reader) - Method in class org.intermine.bio.dataconversion.TreefamConverter
Process the text file
process(File) - Method in class org.intermine.bio.dataconversion.UniprotConverter
Perform the conversion files in the directory
process(Reader) - Method in class org.intermine.bio.dataconversion.UniprotKeywordConverter
Perform the currentFile conversion
process() - Method in class org.intermine.bio.dataconversion.VcfLoaderTask
Process and load the SNP file.
process() - Method in class org.intermine.codegen.JavaModelOutput
Perform the mapping.
process() - Method in class org.intermine.dataconversion.DBConverter
Query from database and write items to the writer.
process(File) - Method in class org.intermine.dataconversion.DirectoryConverter
Perform the conversion files in the directory
process(Reader) - Method in class org.intermine.dataconversion.FileConverter
Perform the currentFile conversion
process(Reader) - Method in class org.intermine.dataconversion.FullXmlConverter
Unmarshal the Items from the input XML file, and write them to the writer.
process(ObjectStore, Source, Source) - Method in class org.intermine.dataloader.ObjectStoreDataLoader
Performs the loading operation, reading data from the given ObjectStore, which must use the same model as the destination IntegrationWriter.
process(ObjectStore, Source, Source, Class<? extends FastPathObject>) - Method in class org.intermine.dataloader.ObjectStoreDataLoader
Loads only a specified class reading data from the given ObjectStore, which must use the same model as the destination IntegrationWriter.
process(Reader) - Method in class org.intermine.metadata.InterMineModelParser
Read source model information in InterMine XML format and construct a InterMine Model object.
process(Reader) - Method in interface org.intermine.metadata.ModelParser
Read source model information and construct a InterMine Model object.
process() - Method in class org.intermine.objectstore.intermine.TorqueModelOutput
Process the schema and put the output in the file.
process() - Method in class org.intermine.task.DirectDataLoaderTask
Called by execute() to process the data.
process() - Method in class org.intermine.task.FileDirectDataLoaderTask
 
process() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
 
process() - Method in class org.intermine.web.logic.widget.GraphWidget
Process the data and create the widget
process() - Method in class org.intermine.web.logic.widget.HTMLWidget
 
process() - Method in class org.intermine.web.logic.widget.TableWidget
Process the data and create the widget
process() - Method in class org.intermine.web.logic.widget.Widget
Process the data and create the widget
process(String, WidgetConfig) - Method in class org.intermine.webservice.server.widget.FlatWidgetProcessor
 
process(String, WidgetConfig) - Method in class org.intermine.webservice.server.widget.JSONWidgetProcessor
 
process(String, WidgetConfig) - Method in interface org.intermine.webservice.server.widget.WidgetProcessor
Process a widget.
process(String, WidgetConfig) - Method in class org.intermine.webservice.server.widget.WidgetProcessorImpl
Process a list called x with a widget y
process(String, WidgetConfig) - Method in class org.intermine.webservice.server.widget.XMLWidgetProcessor
 
processConstraint(PathQuery, String, Map<String, String>, Collection<String>) - Method in class org.intermine.pathquery.PathQueryHandler
Process a constraint from the xml attributes.
processFile(File) - Method in class org.intermine.bio.dataconversion.EnsembSnpLoaderTask
Called by process() once for each File we need to process.
processFile(File) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
Handles each fasta file.
processFile(File) - Method in class org.intermine.bio.dataconversion.VcfLoaderTask
Called by process() once for each File we need to process.
processFile(File) - Method in class org.intermine.task.FileDirectDataLoaderTask
Called by process() once for each File we need to process.
processFile(File) - Method in class org.intermine.task.TSVFileReaderTask
Query all objects of the class given by the className specified in the configurationFile.
processForwardConfig(HttpServletRequest, HttpServletResponse, ForwardConfig) - Method in class org.intermine.web.struts.InterMineRequestProcessor
Overridden to copy errors and messages to session before performing a redirecting forward.
processGroupClause(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a GROUP clause.
processIdentifiers(String, ListCreationInput, Set<String>, Set<String>, InterMineBag) - Method in class org.intermine.webservice.server.lists.ListUploadService
Process the identifiers.
processing() - Method in class org.intermine.bio.dataconversion.UniprotEntry
this check is necessary because the xml attributes may occur in other XML entries
processingFeature() - Method in class org.intermine.bio.dataconversion.UniprotEntry
this check is necessary because the xml attributes may occur in other XML entries.
processItem(DataConverter, Item) - Method in class org.intermine.bio.dataconversion.BioStoreHook
Assigns SO terms and datasets to item, if appropriate.
processItem(DataConverter, Item) - Method in interface org.intermine.dataconversion.DataConverterStoreHook
This method is called before storing an Item.
processLimitClause(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a Limit clause.
processLocationTable(Connection, ResultSet) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Process a featureloc table and create Location objects.
processNewAbstractConstraint(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes an AbstractConstraint.
processNewAbstractValue(AST) - Method in class org.intermine.sql.query.Query
Processes a single AST node that describes an AbstractValue.
processNewField(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a Field.
processNewSafeFunction(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a safe function.
processNewSelect(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a SelectValue.
processNewTypecast(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a typecast.
processNewUnsafeFunction(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes an unsafe function.
processOntology(Reader) - Method in class org.intermine.bio.ontology.OboParser
Parse an OBO file to produce a set of OboTerms.
processOrderClause(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a ORDER clause.
processPreprocess(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.InterMineRequestProcessor
This is called during the processing of every controller.
processQuery(PathQuery) - Static method in class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj
Transform a query from a standard one into one that conforms to the requirements of JSON objects.
processRelation(OboRelation) - Method in class org.intermine.bio.dataconversion.OboConverter
Process and store OboRelations
processRelations(String) - Method in class org.intermine.bio.ontology.OboParser
Parse the relations file generated by the OboEdit reasoner (calculates transitivity)
processResults(List<AcceptanceTestResult>, PrintWriter) - Method in class org.intermine.task.AcceptanceTestTask
Write a formatted HTML summary of the given AcceptanceTestResult objects to the PrintWriter.
processSelectList(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a SELECT list.
processValue(String) - Method in class org.intermine.bio.chado.config.MatchingFieldConfigAction
Process the value to set and return a (possibly) altered version.
processXml(InputStream, Source, Source) - Method in class org.intermine.dataloader.XmlDataLoader
Static method to unmarshall business objects from a given xml file and call store on each.
produce() - Method in class org.intermine.webservice.server.core.ListManager
 
produce() - Method in interface org.intermine.webservice.server.core.Producer
 
produceName() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput
 
produceName() - Method in class org.intermine.webservice.server.lists.ListInput
 
produceName() - Method in class org.intermine.webservice.server.lists.ListRenameInput
 
Producer<T> - Interface in org.intermine.webservice.server.core
The type of functions that take no input and produce a value.
productMap - Variable in class org.intermine.bio.dataconversion.GoConverter
 
Profile - Class in org.intermine.api.profile
Class to represent a user of the webapp The profile is responsible for informing its search repository of all web-searchable objects created or deleted on its watch.
Profile(ProfileManager, String, Integer, String, Map<String, SavedQuery>, Map<String, InterMineBag>, Map<String, ApiTemplate>, String, boolean, boolean) - Constructor for class org.intermine.api.profile.Profile
Construct a Profile
Profile(ProfileManager, String, Integer, String, Map<String, SavedQuery>, Map<String, InterMineBag>, Map<String, InterMineBag>, Map<String, ApiTemplate>, String, boolean, boolean) - Constructor for class org.intermine.api.profile.Profile
Construct a Profile
Profile(ProfileManager, String, Integer, String, Map<String, SavedQuery>, BagSet, Map<String, ApiTemplate>, String, boolean, boolean) - Constructor for class org.intermine.api.profile.Profile
Construct a Profile
Profile(ProfileManager, String, Integer, String, Map<String, SavedQuery>, Map<String, InterMineBag>, Map<String, ApiTemplate>, boolean, boolean) - Constructor for class org.intermine.api.profile.Profile
Construct a profile without an API key
profile - Variable in class org.intermine.api.query.QueryExecutor
The profile to use to find bags from.
profile - Variable in class org.intermine.api.search.SearchRepository
 
PROFILE - Static variable in class org.intermine.web.logic.Constants
Session attribute used to store the user's Profile
profile - Variable in class org.intermine.webservice.server.lists.ListInput
 
profile - Variable in class org.intermine.webservice.server.query.QueryUploadService
 
PROFILE_FORMAT_VERSION - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key used to store profile format version.
ProfileAlreadyExistsException - Exception in org.intermine.api.profile
Exception thrown when attempting to create a profile element with a name that already exists.
ProfileAlreadyExistsException(String) - Constructor for exception org.intermine.api.profile.ProfileAlreadyExistsException
Constructs an ProfileNameAlreadyExistsExceptionException with the specified detail message.
ProfileAlreadyExistsException(Throwable) - Constructor for exception org.intermine.api.profile.ProfileAlreadyExistsException
Constructs an ProfileAlreadyExistsExceptionException with the specified nested throwable.
ProfileAlreadyExistsException(String, Throwable) - Constructor for exception org.intermine.api.profile.ProfileAlreadyExistsException
Constructs an ProfileAlreadyExistsExceptionException with the specified detail message and nested throwable.
ProfileBinding - Class in org.intermine.api.xml
Code for reading and writing Profile objects as XML.
profileCache - Variable in class org.intermine.api.profile.ProfileManager
 
profileId - Variable in class org.intermine.api.profile.StorableBag
 
profileManager - Variable in class org.intermine.api.bag.SharedBagManager
 
profileManager - Variable in class org.intermine.api.InterMineAPI
 
ProfileManager - Class in org.intermine.api.profile
Class to manage and persist user profile data such as saved bags
ProfileManager(ObjectStore, ObjectStoreWriter) - Constructor for class org.intermine.api.profile.ProfileManager
Construct a ProfileManager for the webapp
ProfileManager.ApiPermission - Class in org.intermine.api.profile
A representation of the level of permissions granted to a user.
ProfileManager.ApiPermission.Level - Enum in org.intermine.api.profile
The possible permission levels.
ProfileManager.AuthenticationException - Exception in org.intermine.api.profile
Exception thrown when the authentication fails.
ProfileManager.AuthenticationException(String) - Constructor for exception org.intermine.api.profile.ProfileManager.AuthenticationException
Constructor
ProfileManagerBinding - Class in org.intermine.api.xml
Code for reading and writing ProfileManager objects as XML
ProfileMergeIssues - Class in org.intermine.web.logic.profile
The problems that arose when merging two profiles.
ProfileMergeIssues() - Constructor for class org.intermine.web.logic.profile.ProfileMergeIssues
 
ProfileReadTask - Class in org.intermine.web.task
Task to read an XML file of a webapp userprofiles into a userprofile ObjectStore.
ProfileReadTask() - Constructor for class org.intermine.web.task.ProfileReadTask
 
ProfileWriteTask - Class in org.intermine.web.task
Task to write an XML file of a webapp userprofile object store.
ProfileWriteTask() - Constructor for class org.intermine.web.task.ProfileWriteTask
 
Project - Class in org.intermine.task.project
A class representing the contents of a project.xml file.
Project() - Constructor for class org.intermine.task.project.Project
 
PROJECT_PROPERTIES - Static variable in class org.intermine.task.Dependencies
The file name of the project specific properties file.
ProjectXmlBinding - Class in org.intermine.task.project
Code for reading project.xml files.
PROP_FILE - Static variable in class org.intermine.bio.dataconversion.GFF3Converter
 
PROP_FILE - Static variable in class org.intermine.bio.dataconversion.GoConverter
 
PROPERTIES_ORIGINS - Static variable in class org.intermine.web.logic.Constants
Attribute used to store origin information about properties in the context of this web application.
PropertiesUtil - Class in org.intermine.util
Convenience class for working with global properties
PropertyChangeEvent - Class in org.intermine.api.search
A representation of a notification that a property of a web searchable has changed.
PropertyChangeEvent(WebSearchable) - Constructor for class org.intermine.api.search.PropertyChangeEvent
Constructor.
propertyNames() - Method in class org.intermine.webservice.server.jbrowse.util.NameSpacedProperties
 
propName - Variable in class org.intermine.task.XPathSelect
 
Protein2iprConverter - Class in org.intermine.bio.dataconversion
This parser is use for parsing protein domain assignments and protein domain locations in protein2ipr.dat form InterPro.
Protein2iprConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.Protein2iprConverter
Constructor
ProteinAtlasDisplayer - Class in org.intermine.bio.web.displayer
Protein Atlas Tissue Expression Displayer, showing antibody staining per organ group etc.
ProteinAtlasDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.ProteinAtlasDisplayer
 
ProteinAtlasExpressions - Class in org.intermine.bio.web.model
Protein Atlas Expressions
ProteinAtlasExpressions(ExportResultsIterator) - Constructor for class org.intermine.bio.web.model.ProteinAtlasExpressions
Convert Path results into a List (ProteinAtlasDisplayer.java)
ProteinAtlasExpressions.ByCellCountComparator - Class in org.intermine.bio.web.model
Reorder a TreeMap based on the number of cells contained in Expressions
ProteinAtlasExpressions.ByCellCountComparator() - Constructor for class org.intermine.bio.web.model.ProteinAtlasExpressions.ByCellCountComparator
 
ProteinAtlasExpressions.ByLevelComparator - Class in org.intermine.bio.web.model
Comparator used on Expressions to order them by staining level
ProteinAtlasExpressions.ByLevelComparator() - Constructor for class org.intermine.bio.web.model.ProteinAtlasExpressions.ByLevelComparator
 
ProteinAtlasExpressions.ByOverallLevelComparator - Class in org.intermine.bio.web.model
Reorder a TreeMap based on the overall staining level of the Expressions
ProteinAtlasExpressions.ByOverallLevelComparator() - Constructor for class org.intermine.bio.web.model.ProteinAtlasExpressions.ByOverallLevelComparator
 
ProteinAtlasExpressions.ExpressionList - Class in org.intermine.bio.web.model
Represents a treemap structure of maps of expressions
ProteinAtlasExpressions.ExpressionList(Comparator<String>) - Constructor for class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList
Constructor
ProteinAtlasExpressions.ExpressionList.StainingLevel - Class in org.intermine.bio.web.model
Gives us 'stats' on the overall staining level of the Expressions
ProteinAtlasExpressions.ExpressionList.StainingLevel(ProteinAtlasExpressions.ByLevelComparator) - Constructor for class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList.StainingLevel
 
ProteinAtlasExpressions.ExpressionType - Class in org.intermine.bio.web.model
Represents the type (APE/Staining)
ProteinAtlasExpressions.ExpressionType(String) - Constructor for class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionType
 
ProteinAtlasExpressions.StainingLevelEvaluator - Class in org.intermine.bio.web.model
Determines the "points" staining levels will get
ProteinAtlasExpressions.StainingLevelEvaluator() - Constructor for class org.intermine.bio.web.model.ProteinAtlasExpressions.StainingLevelEvaluator
 
ProteinSequenceDisplayer - Class in org.intermine.bio.web.displayer
Displayer for protein sequence
ProteinSequenceDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.ProteinSequenceDisplayer
Construct with config and the InterMineAPI.
ProteinStructureATMDisplayer - Class in org.intermine.bio.web.displayer
Protein Structure ATM Displayer turning the field into a link that shows the shebang in new window.
ProteinStructureATMDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.ProteinStructureATMDisplayer
 
PROVIDER - Static variable in class org.intermine.web.logic.Constants
The name of the current open-id provider
ProxyCollection<E> - Class in org.intermine.objectstore.proxy
Class which holds a reference to a collection in the database
ProxyCollection(ObjectStore, InterMineObject, String, Class<? extends E>) - Constructor for class org.intermine.objectstore.proxy.ProxyCollection
Construct a ProxyCollection object.
ProxyReference - Class in org.intermine.objectstore.proxy
Class which holds a reference to an object in the database
ProxyReference(ObjectStore, Integer, Class<? extends InterMineObject>) - Constructor for class org.intermine.objectstore.proxy.ProxyReference
Construct a ProxyReference object.
PseudoSet<E> - Class in org.intermine.util
A Set that does not actually contain objects, but provides useful results for the contains method.
PseudoSet() - Constructor for class org.intermine.util.PseudoSet
 
PsiComplexesConverter - Class in org.intermine.bio.dataconversion
Converter to parse complexes.
PsiComplexesConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.PsiComplexesConverter
Constructor
PsiConverter - Class in org.intermine.bio.dataconversion
DataConverter to parse psi data into items Experiments and interactions appear in different files, so we have to keep all experiments until all interactions are processed.
PsiConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.PsiConverter
Constructor
PUBLIC_TAG_LIST - Static variable in class org.intermine.web.struts.InitialiserPlugin
The list of tags that mark something as public
PublicationAnnotationsDisplayer - Class in org.intermine.bio.web.displayer
Display all objects mentioned by publication
PublicationAnnotationsDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.PublicationAnnotationsDisplayer
Construct with config and the InterMineAPI.
PublicationCountsDisplayer - Class in org.intermine.bio.web.displayer
Display publication and number of genes annotated by that publication.
PublicationCountsDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.PublicationCountsDisplayer
Construct with config and the InterMineAPI.
PUBLICIDENTITY - Static variable in class org.intermine.web.task.IssueTokenTask
The identity of the issuing entity (i.e. us)
PublicKeySource - Interface in org.intermine.web.security
An object that can provide public keys by name, or all known keys, or a subset of keys.
PubMedGeneConverter - Class in org.intermine.bio.dataconversion
DataConverter creating items from PubMed data file
PubMedGeneConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.PubMedGeneConverter
 
pubRefId - Variable in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder
 
pureObjects - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
This is a list of the objects that did not merge with anything from a previous data source
pushTag(String) - Method in class org.intermine.webservice.server.output.XMLFormatter
Set the current tag we are working within.
put(String, String) - Method in class org.intermine.api.profile.UserPreferences
 
put(K, V) - Method in class org.intermine.api.util.DevNullMap
 
put(String, Source) - Method in class org.intermine.dataloader.ObjectDescription
Adds a fieldname-source mapping for this ObjectDescription that is not present in the backing database.
put(Object, Object) - Method in class org.intermine.metadata.NonOverrideableProperties
Override put, but do not allow existing values to be changed.
put(K, V) - Method in class org.intermine.util.AlwaysMap
put(E, E) - Method in class org.intermine.util.IdentityMap
put(int, int) - Method in class org.intermine.util.IntToIntMap
Creates a mapping in the object.
put(Integer, Integer) - Method in class org.intermine.util.IntToIntMap
Puts a mapping in the object.
put(E) - Method in class org.intermine.util.ObjectPipe
Adds an Object onto the end of the queue.
put(K, V) - Method in class org.intermine.util.ReferenceMap
put(InterMineObject, ReportObject) - Method in class org.intermine.web.logic.results.ReportObjectFactory
Disable this method.
put(Object, Object) - Method in class org.intermine.webservice.server.jbrowse.util.NameSpacedProperties
 
putAll(Map<? extends String, ? extends String>) - Method in class org.intermine.api.profile.UserPreferences
 
putAll(Map<? extends K, ? extends V>) - Method in class org.intermine.util.AlwaysMap
putAll(Map<? extends E, ? extends E>) - Method in class org.intermine.util.IdentityMap
putAll(Collection<? extends E>) - Method in class org.intermine.util.ObjectPipe
Adds a whole Collection of Objects onto the end of the queue, in the order that the Collection's Iterator presents them.
putAll(Map<? extends K, ? extends V>) - Method in class org.intermine.util.ReferenceMap
putAll(Map<? extends Object, ? extends Object>) - Method in class org.intermine.webservice.server.jbrowse.util.NameSpacedProperties
 
putClean(String, Source) - Method in class org.intermine.dataloader.ObjectDescription
Adds a fieldname-source mapping for this ObjectDescription while keeping it clean.
putQuery(String) - Method in class org.intermine.api.query.MemoryQueryStore
 
putQuery(String) - Method in interface org.intermine.api.query.QueryStore
 

Q

q - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
qc - Variable in class org.intermine.objectstore.query.QueryForeignKey
 
qc - Variable in class org.intermine.objectstore.query.QueryReference
 
qc1 - Variable in class org.intermine.objectstore.query.ClassConstraint
 
qc2 - Variable in class org.intermine.objectstore.query.ClassConstraint
 
qcb - Variable in class org.intermine.objectstore.query.QueryCollectionReference
 
qcObj - Variable in class org.intermine.objectstore.query.QueryCollectionReference
 
qe - Variable in class org.intermine.objectstore.query.SubqueryConstraint
 
qe1 - Variable in class org.intermine.objectstore.query.SimpleConstraint
 
qe2 - Variable in class org.intermine.objectstore.query.SimpleConstraint
 
qn - Variable in class org.intermine.objectstore.query.BagConstraint
 
queries - Variable in class org.intermine.sql.precompute.BestQueryStorer
 
Queries - Class in org.intermine.webservice.server.jbrowse
 
QUERIES_PARAMETER - Static variable in class org.intermine.webservice.server.query.QueryUploadService
The key for the queries parameter
queriesInUnion - Variable in class org.intermine.sql.query.Query
 
Query - Class in org.intermine.objectstore.query
This class provides an implementation-independent abstract representation of a query
Query() - Constructor for class org.intermine.objectstore.query.Query
Empty constructor.
query - Variable in class org.intermine.objectstore.query.ResultsBatches
 
query - Variable in class org.intermine.pathquery.PathQueryHandler
 
query - Variable in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
 
query - Variable in class org.intermine.sql.precompute.BestQueryFallback
 
Query - Class in org.intermine.sql.query
Represents an SQL query in parsed form.
Query() - Constructor for class org.intermine.sql.query.Query
Construct a new Query.
Query(Map<String, AbstractTable>) - Constructor for class org.intermine.sql.query.Query
Construct a new Query.
Query(Map<String, AbstractTable>, List<Query>) - Constructor for class org.intermine.sql.query.Query
Construct a new Query.
Query(String) - Constructor for class org.intermine.sql.query.Query
Construct a new parsed Query from a String.
Query(String, boolean) - Constructor for class org.intermine.sql.query.Query
Construct a new parsed Query from a String.
Query(String, Long) - Constructor for class org.intermine.sql.query.Query
Construct a new parsed Query from a String.
Query(String, boolean, Long) - Constructor for class org.intermine.sql.query.Query
Construct a new parsed Query from a String.
query - Variable in class org.intermine.sql.query.SubQuery
 
query - Variable in class org.intermine.task.RunIqlQueryTask
 
QUERY - Static variable in class org.intermine.web.logic.Constants
Session attribute used to store the current query
QUERY_FOR_GOFASTER - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
query for go faster
QUERY_FOR_PRECOMP - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
query for precomputing
QUERY_NORMAL - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
normal query
QUERY_PARAMETER - Static variable in class org.intermine.webservice.server.query.result.QueryResultRequestParser
Name of parameter with query
QUERY_SUBQUERY_CONSTRAINT - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
subquery in CONSTRAINT
QUERY_SUBQUERY_EXISTS - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
subquery exists
QUERY_SUBQUERY_FROM - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
subquery in FROM
QUERY_TIMEOUT_SECONDS - Static variable in class org.intermine.web.logic.Constants
Period of time to wait for client to poll a running query before cancelling the query.
QUERY_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of class that tracks queries
QUERY_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of table that tracks queries
Queryable - Interface in org.intermine.objectstore.query
An interface for an object that has a SELECT list and a WHERE clause, like a Query.
QueryBuilderChange - Class in org.intermine.web.struts
Action to handle links on main query builder tile.
QueryBuilderChange() - Constructor for class org.intermine.web.struts.QueryBuilderChange
 
QueryBuilderConstraintAction - Class in org.intermine.web.struts
Action to handle button presses on the main tile
QueryBuilderConstraintAction() - Constructor for class org.intermine.web.struts.QueryBuilderConstraintAction
 
QueryBuilderConstraintController - Class in org.intermine.web.struts
Controller for the main constraint editing tile
QueryBuilderConstraintController() - Constructor for class org.intermine.web.struts.QueryBuilderConstraintController
 
QueryBuilderConstraintForm - Class in org.intermine.web.struts
The form used for editing QueryBuilder constraints
QueryBuilderConstraintForm() - Constructor for class org.intermine.web.struts.QueryBuilderConstraintForm
 
QueryBuilderController - Class in org.intermine.web.struts
Controller for the main query builder tile.
QueryBuilderController() - Constructor for class org.intermine.web.struts.QueryBuilderController
 
QueryBuilderSummaryController - Class in org.intermine.web.struts
Controller for the QueryBuilder summary tile.
QueryBuilderSummaryController() - Constructor for class org.intermine.web.struts.QueryBuilderSummaryController
 
QueryBuilderSummaryHelper - Class in org.intermine.web.logic.querybuilder
Methods to generate summary information for a PathQuery for use in display of QueryBuilder summary section.
QueryBuilderViewAction - Class in org.intermine.web.struts
Action to run constructed query.
QueryBuilderViewAction() - Constructor for class org.intermine.web.struts.QueryBuilderViewAction
 
QueryBuilderViewChange - Class in org.intermine.web.struts
Action to handle links on view tile
QueryBuilderViewChange() - Constructor for class org.intermine.web.struts.QueryBuilderViewChange
 
queryCancelled() - Method in interface org.intermine.web.logic.query.QueryMonitor
Called when the query is cancelled.
queryCancelled() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Called when the query is cancelled.
queryCancelledWithError() - Method in interface org.intermine.web.logic.query.QueryMonitor
Called when the query stopped with an error.
queryCancelledWithError() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Called when the query stopped with an error.
QueryCast - Class in org.intermine.objectstore.query
Represents a type cast in a Query.
QueryCast(QueryEvaluable, Class<?>) - Constructor for class org.intermine.objectstore.query.QueryCast
Construct a QueryCast.
queryClass - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
QueryClass - Class in org.intermine.objectstore.query
Represents the database extent of a Java class NOTE - No equals() method is defined for this class and none should be.
QueryClass(Class<? extends FastPathObject>) - Constructor for class org.intermine.objectstore.query.QueryClass
Constructs a QueryClass representing the specified Java class
QueryClass(Set<Class<?>>) - Constructor for class org.intermine.objectstore.query.QueryClass
Constructs a QueryClass representing the specified set of classes
QueryClass(Class<?>...) - Constructor for class org.intermine.objectstore.query.QueryClass
Constructs a QueryClass representing the specified array of classes
QueryClassBag - Class in org.intermine.objectstore.query
An element that can appear in the FROM clause of a query
QueryClassBag(Class<? extends InterMineObject>, Collection<?>) - Constructor for class org.intermine.objectstore.query.QueryClassBag
Constructs a QueryClassBag representing the specified Java class and bag of objects.
QueryClassBag(Set<Class<?>>, Collection<?>) - Constructor for class org.intermine.objectstore.query.QueryClassBag
Constructs a QueryClass representing the specified set of classes and bag of objects.
QueryClassBag(Class<? extends InterMineObject>, ObjectStoreBag) - Constructor for class org.intermine.objectstore.query.QueryClassBag
Constructs a QueryClassBag representing the specified Java class and ObjectStoreBag.
QueryClassBag(Set<Class<?>>, ObjectStoreBag) - Constructor for class org.intermine.objectstore.query.QueryClassBag
Constructs a QueryClass representing the specified set of classes and ObjectStoreBag.
queryClassInQuery - Variable in class org.intermine.web.logic.widget.WidgetLdr
 
QueryClassSelectAction - Class in org.intermine.web.struts
Implementation of Action that processes QueryClass selection form.
QueryClassSelectAction() - Constructor for class org.intermine.web.struts.QueryClassSelectAction
 
QueryClassSelectForm - Class in org.intermine.web.struts
Form bean for selection of a new query class.
QueryClassSelectForm() - Constructor for class org.intermine.web.struts.QueryClassSelectForm
 
queryClassToString(StringBuffer, QueryClass, Query, DatabaseSchema, int, SqlGenerator.State) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a QueryClass to a String.
QueryCloner - Class in org.intermine.objectstore.query
This is a static class that provides a method to clone a Query object.
QueryCollectionPathExpression - Class in org.intermine.objectstore.query
An element that can appear in the SELECT clause of a query, representing extra data to be collected for the Results - namely a collection or reference referenced in an object in the results.
QueryCollectionPathExpression(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryCollectionPathExpression
Constructs a QueryCollectionPathExpression representing a reference from the given QueryClass to the given field name.
QueryCollectionPathExpression(QueryClass, String, Class<?>...) - Constructor for class org.intermine.objectstore.query.QueryCollectionPathExpression
Constructs a QueryCollectionPathExpression representing a reference from the given QueryClass to the given field name, constrained to be a particular subclass.
queryCollectionPathExpressionToString(Query, List<Object>, QueryCollectionPathExpression) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Converts a QueryObjectPathExpression into a String.
QueryCollectionReference - Class in org.intermine.objectstore.query
Represents a field of a QueryClass that is a collection
QueryCollectionReference(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryCollectionReference
Constructs a QueryCollectionReference representing the specified field of a QueryClass
QueryCollectionReference(QueryClassBag, String) - Constructor for class org.intermine.objectstore.query.QueryCollectionReference
Constructs a QueryCollectionReference representing the specified field of a QueryClassBag
QueryCollectionReference(InterMineObject, String) - Constructor for class org.intermine.objectstore.query.QueryCollectionReference
Constructs a QueryCollectionReference representing the specified field of an object
queryCompleted() - Method in interface org.intermine.web.logic.query.QueryMonitor
Called when the query has completed.
queryCompleted() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Called when the query has completed.
QueryCountQueryMonitor - Class in org.intermine.web.logic.session
A QueryMonitor that maintains a timeout and is used when counting the number of rows a query returns.
QueryCountQueryMonitor(int, Query) - Constructor for class org.intermine.web.logic.session.QueryCountQueryMonitor
Construct a new instance of QueryCountQueryMonitor.
QueryCreator - Class in org.intermine.objectstore.query
Class that helps build queries or parts of queries for common situations.
queryEquivalentObjects(InterMineObject, Source) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Returns a Set of objects that are equivalent to the given object, according to the primary keys defined by the given Source.
queryEquivalentObjects(InterMineObject, Source) - Method in class org.intermine.dataloader.BatchingFetcher
Returns a Set of objects that are equivalent to the given object, according to the primary keys defined by the given Source.
queryEquivalentObjects(InterMineObject, Source) - Method in interface org.intermine.dataloader.EquivalentObjectFetcher
Returns a Set of objects that are equivalent to the given object, according to the primary keys defined by the given Source.
queryEquivalentObjects(InterMineObject, Source) - Method in class org.intermine.dataloader.HintingFetcher
Returns a Set of objects that are equivalent to the given object, according to the primary keys defined by the given Source.
QueryEvaluable - Interface in org.intermine.objectstore.query
An element that can be evaluated for comparison (one that represents an atomic type)
queryEvaluableToString(StringBuffer, QueryEvaluable, Query, SqlGenerator.State) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a QueryEvaluable into a String suitable for an SQL query String.
QueryExecutor - Class in org.intermine.api.query
Common superclass of query executors that holds cache of pathToQueryNode maps per query.
QueryExecutor() - Constructor for class org.intermine.api.query.QueryExecutor
 
queryExperimentsInvolvingGene(String, ObjectStore) - Static method in class org.flymine.web.MicroArrayHelper
 
QueryExpression - Class in org.intermine.objectstore.query
Represents an arithmetic or substring expression, analogous to those in SQL
QueryExpression(QueryEvaluable, int, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.QueryExpression
Constructs an arithmetic QueryExpression from two evaluable items
QueryExpression(QueryEvaluable, QueryEvaluable, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.QueryExpression
Constructs a substring QueryExpression from a QueryEvaluable and start and length QueryEvaluables
QueryExpression(int, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.QueryExpression
Constructs a String QueryExpression to perform upper and lowercase conversions.
queryExpressionToString(Query, QueryExpression, List<Object>) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Converts a QueryExpression into a String.
QueryField - Class in org.intermine.objectstore.query
Represents a QueryClass field that is neither a collection or reference to another business object.
QueryField(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryField
Constructs a QueryField representing the specified field of a QueryClass
QueryField(Query, QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryField
Constructs a QueryField representing the specified field of the specified QueryClass, as seen outside the specified subquery.
QueryField(Query, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.QueryField
Constructs a QueryField representing the specified entry from the SELECT list of the specified subquery.
QueryField(QueryClassBag) - Constructor for class org.intermine.objectstore.query.QueryField
Constructs the id QueryField for the given QueryClassBag.
QueryField(FromElement, String, String, Class<?>) - Constructor for class org.intermine.objectstore.query.QueryField
Constructs a QueryField object - intended for cloning operations.
QueryForeignKey - Class in org.intermine.objectstore.query
Represents the ID of a field of a QueryClass that is a business object
QueryForeignKey(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryForeignKey
Constructs a QueryForeignKey representing the specified field of a QueryClass
QueryForm - Class in org.intermine.web.struts
Action form that holds query XML.
QueryForm() - Constructor for class org.intermine.web.struts.QueryForm
 
queryForTypesInCollection(InterMineObject, String, ObjectStore) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
Search for the classes in a collection for a given InterMineObject, for example find all of the sub-classes of Employee in the Department.employees collection of a given Department.
QueryFunction - Class in org.intermine.objectstore.query
A QueryFunction represents an aggregate
QueryFunction(QueryEvaluable, int) - Constructor for class org.intermine.objectstore.query.QueryFunction
 
QueryFunction(QueryEvaluable, int, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.QueryFunction
Constructor for functions that take two parameters.
QueryFunction() - Constructor for class org.intermine.objectstore.query.QueryFunction
Creates a COUNT aggregate function.
QueryGenUtil - Class in org.intermine.objectstore.querygen
Utility methods for paths.
QueryGenUtil.QueryAndClass - Class in org.intermine.objectstore.querygen
Class to allow returning of two arguments from a method.
QueryGenUtil.QueryAndClass(Query, Class<?>) - Constructor for class org.intermine.objectstore.querygen.QueryGenUtil.QueryAndClass
Constructor.
QueryHelper - Class in org.intermine.objectstore.query
Static methods to assist with query generation from front end.
queryHistory - Variable in class org.intermine.api.profile.Profile
 
QueryListAppendService - Class in org.intermine.webservice.server.query
Append items to a list from the results of a query.
QueryListAppendService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryListAppendService
Constructor.
QueryListAppendServlet - Class in org.intermine.webservice.server.query
Runs the query-to-list service to run queries and save them as lists.
QueryListAppendServlet() - Constructor for class org.intermine.webservice.server.query.QueryListAppendServlet
 
QueryLogger - Class in org.intermine.sql.logging
Provides a logging facility for a Query
queryMicroArrayResults(String, String, ObjectStore) - Static method in class org.flymine.web.MicroArrayHelper
For a given gene and experiment retrieve results and assays and displayOrder attribute.
QueryMonitor - Interface in org.intermine.web.logic.query
Interface passed to SessionMethods runQuery method which is polled every so-often while the query runs in order to decide whether or not to cancel the query.
QueryMonitorTimeout - Class in org.intermine.web.logic.query
QueryMonitor that cancels a query after a given timeout period.
QueryMonitorTimeout(int) - Constructor for class org.intermine.web.logic.query.QueryMonitorTimeout
Construct a new instance of QueryMonitorTimeout.
queryName - Variable in class org.intermine.web.struts.SaveQueryForm
 
QueryNode - Interface in org.intermine.objectstore.query
An element that can appear in the SELECT, ORDER BY or GROUP BY clause of a query.
QueryObjectPathExpression - Class in org.intermine.objectstore.query
An element that can appear in the SELECT clause of a query, representing extra data to be collected for the Results - namely a object referenced by some other object in the results.
QueryObjectPathExpression(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryObjectPathExpression
Constructs a QueryObjectPathExpression representing an object reference from the given QueryClass to the given fieldname.
QueryObjectPathExpression(QueryClass, String, Class<?>...) - Constructor for class org.intermine.objectstore.query.QueryObjectPathExpression
Constructs a QueryObjectPathExpression representing an object reference from the given QueryClass to the given fieldname, constrained to be a particular subclass.
queryObjectPathExpressionToString(Query, List<Object>, QueryObjectPathExpression) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Converts a QueryObjectPathExpression into a String.
QueryObjectReference - Class in org.intermine.objectstore.query
Represents a field of a QueryClass that is a business object
QueryObjectReference(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryObjectReference
Constructs a QueryObjectReference representing the specified field of a QueryClass
QueryOptimiser - Class in org.intermine.sql.precompute
A static class providing the code to optimise a query, given a database (presumably with a table describing the available precomputed tables).
QueryOptimiser.AbstractTableComparator - Class in org.intermine.sql.precompute
Compares two AbstractTables using their equalsIgnoreAlias() method.
QueryOptimiser.AbstractTableComparator() - Constructor for class org.intermine.sql.precompute.QueryOptimiser.AbstractTableComparator
Constructor.
QueryOptimiserContext - Class in org.intermine.sql.precompute
A class describing settings for the optimiser.
QueryOptimiserContext() - Constructor for class org.intermine.sql.precompute.QueryOptimiserContext
 
QueryOptimiserException - Exception in org.intermine.sql.precompute
An Exception that may be thrown by a QueryOptimiser method.
QueryOptimiserException() - Constructor for exception org.intermine.sql.precompute.QueryOptimiserException
Constructs an QueryOptimiserException
QueryOptimiserException(String) - Constructor for exception org.intermine.sql.precompute.QueryOptimiserException
Constructs an QueryOptimiserException with the specified detail message.
QueryOptimiserException(Throwable) - Constructor for exception org.intermine.sql.precompute.QueryOptimiserException
Constructs an QueryOptimiserException with the specified nested throwable.
QueryOptimiserException(String, Throwable) - Constructor for exception org.intermine.sql.precompute.QueryOptimiserException
Constructs an QueryOptimiserException with the specified detail message and nested throwable.
QueryOrderable - Interface in org.intermine.objectstore.query
An element that can appear in the ORDER BY clause of a query.
QueryParseTimeoutException - Exception in org.intermine.sql.query
Exception thrown when parsing a query from SQL string to org.intermine.sql.Query object.
QueryParseTimeoutException() - Constructor for exception org.intermine.sql.query.QueryParseTimeoutException
 
QueryPathExpression - Interface in org.intermine.objectstore.query
An element that can appear in the SELECT clause of a query, representing extra data to be collected for the Results, usually in a separate database operation.
QueryPathExpressionWithSelect - Interface in org.intermine.objectstore.query
A Path Expression that has a Select list.
QueryReference - Class in org.intermine.objectstore.query
Represents a field of a QueryClass that is a non-primitive type.
QueryReference() - Constructor for class org.intermine.objectstore.query.QueryReference
 
queryReferenceToString(Query, QueryReference, List<Object>) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Converts a QueryReference into a String.
QueryRemovalService - Class in org.intermine.webservice.server.query
A service that removes a saved query from profile's collection of saved queries.
QueryRemovalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryRemovalService
 
QueryRequestParser - Class in org.intermine.webservice.server.query
Processes query request parameters.
QueryRequestParser(QueryStore, HttpServletRequest) - Constructor for class org.intermine.webservice.server.query.QueryRequestParser
RequestProcessor constructor.
QueryResultInput - Class in org.intermine.webservice.server.query.result
QueryServiceInput is parameter object representing parameters for QueryResultService web service.
QueryResultInput() - Constructor for class org.intermine.webservice.server.query.result.QueryResultInput
 
QueryResultLinkGenerator - Class in org.intermine.webservice.server.query.result
Class that implements generating links for QueryResultService web service.
QueryResultLinkGenerator() - Constructor for class org.intermine.webservice.server.query.result.QueryResultLinkGenerator
 
QueryResultRequestParser - Class in org.intermine.webservice.server.query.result
Processes service request.
QueryResultRequestParser(QueryStore, HttpServletRequest) - Constructor for class org.intermine.webservice.server.query.result.QueryResultRequestParser
RequestProcessor constructor.
QueryResultService - Class in org.intermine.webservice.server.query.result
Executes query and returns results.
QueryResultService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.result.QueryResultService
Constructor
QueryResultServlet - Class in org.intermine.webservice.server.query.result
Servlet that runs QueryResultService.
QueryResultServlet() - Constructor for class org.intermine.webservice.server.query.result.QueryResultServlet
 
QueryRetrieverService - Class in org.intermine.webservice.server.query
A service that retrieves a stored query by qid.
QueryRetrieverService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryRetrieverService
 
QuerySelectable - Interface in org.intermine.objectstore.query
An element that can appear in the SELECT clause of a query.
QueryService - Class in org.intermine.webservice.client.services
The QueryService class provides a mechanism for sending data queries to an InterMine webservice, and retrieving and parsing the results.
QueryService(String, String) - Constructor for class org.intermine.webservice.client.services.QueryService
Constructor.
QueryService.NumericSummary - Class in org.intermine.webservice.client.services
Result format for Numeric Summary information.
QueryService.QueryRequest - Class in org.intermine.webservice.client.services
The request class for handling queries - in particular this class is responsible for handling the query parameters.
QueryService.QueryRequest(Request.RequestType, String, ContentType) - Constructor for class org.intermine.webservice.client.services.QueryService.QueryRequest
Constructor.
queryStore - Variable in class org.intermine.api.InterMineAPI
 
QueryStore - Interface in org.intermine.api.query
 
QueryStoreException - Exception in org.intermine.api.query
 
QueryStoreException(String, Exception) - Constructor for exception org.intermine.api.query.QueryStoreException
 
QueryStoreException(String) - Constructor for exception org.intermine.api.query.QueryStoreException
 
QueryStoreService - Class in org.intermine.webservice.server.query
A service that stores a query and associates it with an id.
QueryStoreService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryStoreService
 
queryString - Variable in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
 
queryString - Variable in class org.intermine.sql.precompute.BestQueryFallback
 
QueryToListService - Class in org.intermine.webservice.server.query
A service for transforming a query, represented as a PathQuery serialised to XML, to a list.
QueryToListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryToListService
Constructor.
QueryToListServlet - Class in org.intermine.webservice.server.query
Runs the query-to-list service to run queries and save them as lists.
QueryToListServlet() - Constructor for class org.intermine.webservice.server.query.QueryToListServlet
 
queryToPathToQueryNode - Static variable in class org.intermine.api.query.QueryExecutor
A cache of pathToQueryNode maps that is shared between subclasses of QueryExecutor.
QueryTrack - Class in org.intermine.api.tracker.track
 
QueryTrack(String, String, String, Timestamp) - Constructor for class org.intermine.api.tracker.track.QueryTrack
 
QUERYTRACK - Static variable in class org.intermine.api.tracker.xml.QueryTrackBinding
label for XML
QueryTrackBinding - Class in org.intermine.api.tracker.xml
 
QueryTracker - Class in org.intermine.api.tracker
 
QueryTracker(Connection, Queue<Track>) - Constructor for class org.intermine.api.tracker.QueryTracker
Build a query tracker
QUERYTRACKS - Static variable in class org.intermine.api.tracker.xml.QueryTrackBinding
label for XML
QueryUpdateService - Class in org.intermine.webservice.server.query
Same in all respects as the upload service, but this class overwrites queries with the provided names.
QueryUpdateService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryUpdateService
 
QueryUploadService - Class in org.intermine.webservice.server.query
A service to enable queries to be uploaded programmatically.
QueryUploadService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryUploadService
Constructor.
QueryUploadServlet - Class in org.intermine.webservice.server.query
Runs the query Upload Service to handle user query uploads.
QueryUploadServlet() - Constructor for class org.intermine.webservice.server.query.QueryUploadServlet
 
QueryValue - Class in org.intermine.objectstore.query
Represents a constant in a Query
QueryValue(Object) - Constructor for class org.intermine.objectstore.query.QueryValue
Construct a QueryValue
queue - Variable in class org.intermine.util.ReferenceMap
 
queueMessage(MailAction) - Static method in class org.intermine.web.context.InterMineContext
Queue up a message to an emailer.
QuickSearch - Class in org.intermine.webservice.server.search
A service that runs key-word searches.
QuickSearch(InterMineAPI, ServletContext) - Constructor for class org.intermine.webservice.server.search.QuickSearch
 
QuickSearchJSONProcessor - Class in org.intermine.webservice.server.search
A class that renders quick search results as JSON.
QuickSearchJSONProcessor() - Constructor for class org.intermine.webservice.server.search.QuickSearchJSONProcessor
 
QuickSearchResultProcessor - Interface in org.intermine.webservice.server.search
The type of objects that can handle keyword search results.
QuickSearchServlet - Class in org.intermine.webservice.server.search
 
QuickSearchServlet() - Constructor for class org.intermine.webservice.server.search.QuickSearchServlet
 
QuickSearchTextProcessor - Class in org.intermine.webservice.server.search
A result processor that outputs results as plain text.
QuickSearchTextProcessor(String) - Constructor for class org.intermine.webservice.server.search.QuickSearchTextProcessor
 
QuickSearchXMLProcessor - Class in org.intermine.webservice.server.search
A result processor that outputs results as XML.
QuickSearchXMLProcessor() - Constructor for class org.intermine.webservice.server.search.QuickSearchXMLProcessor
 

R

rand - Static variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
random - Static variable in class org.intermine.web.task.LoadDefaultTemplatesTask
 
Range - Interface in org.intermine.api.query.range
 
range(int, int) - Method in class org.intermine.objectstore.query.Results
Returns a range of rows of results.
range(int, int) - Method in class org.intermine.objectstore.query.SingletonResults
Returns a range of rows of results.
RANGE_DEFINITIONS - Static variable in class org.intermine.modelproduction.MetadataManager
Description of range type columns defined in the database.
rangeConstraint - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
RangeHelper - Interface in org.intermine.api.query
 
rangeHelpers - Static variable in class org.intermine.api.query.MainHelper.RangeConfig
 
rangeOp - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
ranges - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
RateLimitException - Exception in org.intermine.webservice.server.exceptions
Exception representation for denying service based on rate limits.
RateLimitException(String, int) - Constructor for exception org.intermine.webservice.server.exceptions.RateLimitException
Constructor
RateLimitHistory - Class in org.intermine.webservice.server.core
A class for making sure that certain resources don't get hammered.
RateLimitHistory(int, int) - Constructor for class org.intermine.webservice.server.core.RateLimitHistory
Constructor
ReactomeConverter - Class in org.intermine.bio.dataconversion
 
ReactomeConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.ReactomeConverter
Constructor
ReactomePostProcess - Class in org.intermine.bio.postprocess
Copy over Protein.pathways to Gene.pathways
ReactomePostProcess(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.ReactomePostProcess
Create a new instance of BioPAXPostProcess.
read() - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream
 
read(byte[], int, int) - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream
 
readBagQueryConfig(Model, InputStream) - Static method in class org.intermine.api.bag.BagQueryHelper
Read the bag query configuration from the given stream.
readConfig(String) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
Read pid configurations from entrezIdResolver_config.properties in resources dir
readConfig() - Method in class org.intermine.bio.dataconversion.GFF3Converter
read in config file
readConfig() - Method in class org.intermine.bio.ontology.OboParser
Parses config file for valid prefixes, eg.
readGenes(Reader) - Method in class org.intermine.bio.dataconversion.TreefamConverter
Read genes file.
readKeys(Model, Properties) - Static method in class org.intermine.api.config.ClassKeyHelper
Read class keys from a properties into a map from classname to set of available keys.
readLargeBinary(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager
Returns an InputStream object with which to read a large binary value from the database.
readOneTestConfig(LineNumberReader) - Static method in class org.intermine.task.AcceptanceTestTask
Read and return one AcceptanceTest object from the given Reader.
ReadPreferencesService - Class in org.intermine.webservice.server.user
A service for reading the current state of a user's preferences.
ReadPreferencesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.ReadPreferencesService
 
readRelations(BufferedReader) - Method in class org.intermine.bio.ontology.OboParser
This method reads relations calculated by the GO2Link script in OBOEdit.
ReadResourceTask - Class in org.intermine.task
A Task that reads a resource (from the class path) and sets a property with its contents.
ReadResourceTask() - Constructor for class org.intermine.task.ReadResourceTask
 
readTerms(BufferedReader) - Method in class org.intermine.bio.ontology.OboParser
Read DAG input line by line to generate hierarchy of DagTerms.
readWebProperties(Properties) - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
ReadWriteJSONService - Class in org.intermine.webservice.server.core
Convenience for services that need to combine JSON service behaviour with strict RW authorisation.
ReadWriteJSONService(InterMineAPI) - Constructor for class org.intermine.webservice.server.core.ReadWriteJSONService
Construct a read/write service.
realiseObjects(Collection<Item>, Model, boolean) - Static method in class org.intermine.xml.full.FullParser
Create business objects from a collection of Items.
realiseObjects(Collection<Item>, Model, boolean, boolean) - Static method in class org.intermine.xml.full.FullParser
Create business objects from a collection of Items.
ReallyFlatIterator - Class in org.intermine.api.results.flatouterjoins
An Iterator that flattens the contents of another Iterator.
ReallyFlatIterator(Iterator) - Constructor for class org.intermine.api.results.flatouterjoins.ReallyFlatIterator
Constructs a ReallyFlatIterator from another Iterator.
rebuildClassIndexes() - Method in class org.intermine.web.autocompletion.LuceneIndex
rebuild all indexes from LuceneObjectClasses in the map
receiveEvent(ChangeEvent) - Method in class org.intermine.api.search.SearchRepository
 
receiveEvent(ChangeEvent) - Method in interface org.intermine.api.search.WebSearchWatcher
Receive notification of a change to a WebSearchable somewhere in the universe.
recentSequences - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
reconstruct(String) - Method in class org.intermine.sql.precompute.LimitOffsetQuery
Reconstruct a SQL string, given this alternative SQL query-part.
reconstructAbstractConstraint(AbstractConstraint, Table, Map<AbstractValue, SelectValue>, Set<AbstractTable>, boolean, Field, int, Field, boolean, boolean) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Reconstructs an AbstractConstraint object, using reconstructAbstractValue.
reconstructAbstractConstraints(Set<AbstractConstraint>, Table, Map<AbstractValue, SelectValue>, Set<AbstractTable>, boolean, Set<AbstractConstraint>, Set<AbstractConstraint>, Field, int, Field, boolean, boolean) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Populates the WHERE list of a new Query object, given the old Query's WHERE (or HAVING) list to use as a reference.
reconstructAbstractValue(AbstractValue, Table, Map<AbstractValue, SelectValue>, Set<AbstractTable>, boolean) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Reconstructs an AbstractValue, to form the part of an SQL Query that has been replaced with a PrecomputedTable.
reconstructAbstractValues(Collection<AbstractValue>, Table, Map<AbstractValue, SelectValue>, Set<AbstractTable>, boolean, Collection<AbstractValue>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Reconstructs a Collection of AbstractValue objects, calling reconstructAbstractValue on each one before adding it to another Collection.
reconstructSelectValues(List<SelectValue>, Table, Map<AbstractValue, SelectValue>, Set<AbstractTable>, boolean, Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Populates the SELECT list of a new Query object, given an old Query's SELECT list to use as a reference, a valueMap (to pass to reconstructAbstractValue), and a Table to represent the PrecomputedTable.
recordError(String, HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Record an error.
recordError(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineAction
Add the given ActionMessage as an error for this Action
recordError(ActionMessage, HttpServletRequest, Exception) - Method in class org.intermine.web.struts.InterMineAction
Add the given ActionMessage as an error for this Action
recordError(ActionMessage, HttpServletRequest, Exception, Logger) - Method in class org.intermine.web.struts.InterMineAction
Add the given ActionMessage as an error for this Action and log the error
recordError(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineDispatchAction
Add the given ActionMessage as an error for this Action
recordError(ActionMessage, HttpServletRequest, Exception) - Method in class org.intermine.web.struts.InterMineDispatchAction
Add the given ActionMessage as an error for this Action
recordError(ActionMessage, HttpServletRequest, Exception, Logger) - Method in class org.intermine.web.struts.InterMineDispatchAction
Add the given ActionMessage as an error for this Action and log the error
recordError(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineLookupDispatchAction
Add the given ActionMessage as an error for this Action
recordError(ActionMessage, HttpServletRequest, Exception) - Method in class org.intermine.web.struts.InterMineLookupDispatchAction
Add the given ActionMessage as an error for this Action
recordError(ActionMessage, HttpServletRequest, Exception, Logger) - Method in class org.intermine.web.struts.InterMineLookupDispatchAction
Add the given ActionMessage as an error for this Action and log the error
recordMessage(String, HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Record a message that will be stored in the session until it is displayed to the user.
recordMessage(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineAction
Add the given ActionMessage as a message for this Action
recordMessage(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineDispatchAction
Add the given ActionMessage as a message for this Action
recordMessage(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineLookupDispatchAction
Add the given ActionMessage as a message for this Action
recordRequest(String) - Method in class org.intermine.webservice.server.core.RateLimitHistory
Record that a request was made.
recursiveOptimise(Set<PrecomputedTable>, Query, BestQuery, Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Recursively optimises the query, given the set of precomputed tables, and updates the BestQuery object with each Query found.
recursiveOptimiseCheckSubquery(Set<PrecomputedTable>, Query, BestQuery) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Recursively optimises the query, given the set of precomputed tables, and updates the BestQuery object with each Query found.
RedirectManager - Class in org.intermine.model.testmodel.web
 
RedirectManager(Properties) - Constructor for class org.intermine.model.testmodel.web.RedirectManager
 
ref - Variable in class org.intermine.objectstore.query.ContainsConstraint
 
REFERENCE - Static variable in class org.intermine.api.tag.TagTypes
Reference.
reference(Command) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
reference(Command) - Method in class org.intermine.webservice.server.jbrowse.genomic.Engine
 
Reference - Class in org.intermine.xml.full
Representation of an Reference in an object
Reference() - Constructor for class org.intermine.xml.full.Reference
Constructor
Reference(String, String) - Constructor for class org.intermine.xml.full.Reference
Construnctor
REFERENCE_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
The lists to subtract from
referencedClassDesc - Variable in class org.intermine.metadata.ReferenceDescriptor
 
ReferenceDescriptor - Class in org.intermine.metadata
Describes a field that references a single other class (i.e. not a collection of objects).
ReferenceDescriptor(String, String, String) - Constructor for class org.intermine.metadata.ReferenceDescriptor
Construct a ReferenceDescriptor.
referencedType - Variable in class org.intermine.metadata.ReferenceDescriptor
 
ReferenceList - Class in org.intermine.xml.full
Representation of a field in an object.
ReferenceList() - Constructor for class org.intermine.xml.full.ReferenceList
Constructor
ReferenceList(String) - Constructor for class org.intermine.xml.full.ReferenceList
Constructor
ReferenceList(String, List<String>) - Constructor for class org.intermine.xml.full.ReferenceList
Constructor
ReferenceMap<K,V> - Class in org.intermine.util
This is a Map implementation designed specifically for people intending to create a cache.
ReferenceMap() - Constructor for class org.intermine.util.ReferenceMap
 
ReferenceMap.ReferenceWithKey<K> - Interface in org.intermine.util
Interface for entries in the map.
refIds - Variable in class org.intermine.xml.full.ReferenceList
 
refsAndCollections - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler
 
RegionParseException - Exception in org.intermine.bio.web.logic
 
RegionParseException(String) - Constructor for exception org.intermine.bio.web.logic.RegionParseException
 
register(String, String) - Method in class org.intermine.web.logic.export.http.TableExporterFactory
Register exporter.
registerObject(Object) - Static method in class org.intermine.util.ShutdownHook
Registers an object with the shutdown hook.
registerOffset(Query, int, DatabaseSchema, Database, Object, Map<Object, String>) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Registers an offset for a given query.
registerRequestId(Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
This method registers a Thread with a request ID.
registerStatement(Statement) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
This method registers a Statement with the current Thread's request ID, or throws an exception if that request is black-listed, or does nothing if no request ID is present for this Thread.
Registrar - Class in org.intermine.web.struts
A class to handle registration of mines with a registry service.
Registrar(Properties) - Constructor for class org.intermine.web.struts.Registrar
Constructor
RegulatoryRegionsDisplayer - Class in org.intermine.bio.web.displayer
TODO: merge this with OverlappingFeaturesDisplayer to reuse common functionality (preferrably wo/ creating another table type on a report page
RegulatoryRegionsDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.RegulatoryRegionsDisplayer
Construct with config and the InterMineAPI.
rejectInvitation(SharingInvite) - Static method in class org.intermine.api.bag.SharedBagManager
Reject this invitation.
RELATED_DATA_CONSTRAINT_1 - Static variable in class org.intermine.api.config.Constants
Constraint for related data template
RELATED_DATA_CONSTRAINT_2 - Static variable in class org.intermine.api.config.Constants
Constraint for related data template
RELATED_DATA_TEMPLATE - Static variable in class org.intermine.api.config.Constants
queries for data related to current object
relations - Variable in class org.intermine.bio.ontology.OboParser
All relations
relationType() - Method in class org.intermine.metadata.AttributeDescriptor
Return an integer describing the type of relationship this field represents, where relationship types are 1:1, 1:N, N:1, M:N and "not a relationship".
relationType() - Method in class org.intermine.metadata.CollectionDescriptor
Return an integer describing the type of relationship this field represents, where relationship types are 1:1, 1:N, N:1, M:N and "not a relationship".
relationType() - Method in class org.intermine.metadata.FieldDescriptor
Return an integer describing the type of relationship this field represents, where relationship types are 1:1, 1:N, N:1, M:N and "not a relationship".
relationType() - Method in class org.intermine.metadata.ReferenceDescriptor
Return an integer describing the type of relationship this field represents, where relationship types are 1:1, 1:N, N:1, M:N and "not a relationship".
RelativeComplement - Class in org.intermine.api.bag.operations
 
RelativeComplement(Model, Profile, Collection<InterMineBag>, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.RelativeComplement
 
releaseConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Allows one to put a connection back.
releaseConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Allows one to put a connection back.
ReleaseEtagFilter - Class in org.intermine.web.filters
Return responses tagged with the release version.
ReleaseEtagFilter() - Constructor for class org.intermine.web.filters.ReleaseEtagFilter
 
releaseGoFaster() - Method in class org.intermine.api.results.ExportResultsIterator
Switches off the goFaster mode in the objectstore for this query.
releaseGoFaster() - Method in class org.intermine.api.results.WebResults
Calls ObjectStore.releaseGoFaster() if this object wraps a Results object from an ObjectStoreInterMineImpl.
releaseGoFaster(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Releases the resources used by goFaster().
releaseResources(ResultSet, Statement) - Method in class org.intermine.api.tracker.AbstractTracker
Close the result set and statement objects specified in input
releaseResources() - Method in class org.intermine.api.tracker.xml.TrackHandler
 
remapAliases(Map<AbstractTable, AbstractTable>, Set<AbstractTable>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Alters all the aliases of the tables being mapped to, to equal the alias of the table mapping to them.
remapAliasesToAvoidPrecomputePrefix(Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Remaps the aliases of any table that starts with the ALIAS_PREFIX, to avoid clashes with future precomputed tables.
RemoteMine - Class in org.intermine.api.mines
An object that represents an InterMine application hosted somewhere else.
RemoteMine(String, MineRequester, int) - Constructor for class org.intermine.api.mines.RemoteMine
Create a representation of a remotely accessible mine.
remove(Object) - Method in class org.intermine.api.profile.UserPreferences
 
remove() - Method in class org.intermine.api.results.ExportResultsIterator
This method is not supported.
remove() - Method in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator
This operation is not supported.
remove(Object) - Method in class org.intermine.util.AlwaysMap
remove() - Method in class org.intermine.util.CombinedIterator
This operation is not supported.
remove(Object) - Method in class org.intermine.util.IdentityMap
remove() - Method in class org.intermine.util.ObjectPipe
remove(Object) - Method in class org.intermine.util.PseudoSet
remove(Object) - Method in class org.intermine.util.ReferenceMap
remove() - Method in class org.intermine.util.SynchronisedIterator
remove(Object) - Method in class org.intermine.webservice.client.lists.ItemList
 
remove(Object) - Method in class org.intermine.webservice.client.results.ResultRowList
 
remove(int) - Method in class org.intermine.webservice.client.results.ResultRowList
 
remove() - Method in class org.intermine.webservice.server.core.TableRowIterator
 
remove() - Method in class org.intermine.webservice.server.output.FilteringResultIterator
 
remove() - Method in class org.intermine.webservice.server.output.JSONDataTableRowIterator
 
remove() - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Remove is not supported.
remove() - Method in class org.intermine.webservice.server.output.JSONRowIterator
 
remove() - Method in class org.intermine.webservice.server.output.MinimalJsonIterator
 
removeAll(Collection<?>) - Method in class org.intermine.util.PseudoSet
removeAll(Collection) - Method in class org.intermine.webservice.client.lists.ItemList
 
removeAll(Collection<?>) - Method in class org.intermine.webservice.client.results.ResultRowList
 
removeAllFromBag(ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Removes a collection of elements from an ObjectStoreBag, delegate to internal ObjectStoreWriter.
removeAllFromBag(ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Removes a collection of elements from an ObjectStoreBag.
removeAllFromBag(ObjectStoreBag, Collection<Integer>) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Removes a collection of elements from an ObjectStoreBag.
removeAllFromBagWithConnection(Connection, ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Removes elements from the given bag.
removeAllInvitesBy(Integer) - Method in class org.intermine.api.bag.SharedBagManager
Removes all invitations to share resources that were issued by the user with the given id.
removeAllIrrelevant() - Method in class org.intermine.pathquery.PathQuery
Removes everything from this query that is irrelevant, and therefore making the query invalid.
removeAllSharesInvolving(Integer) - Method in class org.intermine.api.bag.SharedBagManager
Removes all shares from or to the user with the given id.
removeAllTables(Connection) - Static method in class org.intermine.sql.DatabaseUtil
Removes every single table from the database given.
removeAllUnder(String) - Method in class org.intermine.pathquery.PathQuery
Removes everything under a given path from the query, such that if the query was valid before, it will be valid after this method.
removeAllVariablesExcept(Collection<String>) - Method in class org.intermine.pathquery.LogicExpression
Remove any variables that aren't in the given set.
removeAttribute(String) - Method in class org.intermine.xml.full.Item
Remove a attribute of the specified name if it exists.
removeCollection(String) - Method in class org.intermine.xml.full.Item
Remove a collection of the specified name if it exists.
removeConstraint(Constraint) - Method in class org.intermine.objectstore.query.ConstraintSet
Remove specified constraint
removeConstraint(PathConstraint) - Method in class org.intermine.pathquery.PathQuery
Removes a constraint from this query.
removeConstraint(PathConstraint) - Method in class org.intermine.template.TemplateQuery
Removes a constraint from this query.
removeConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Remove a constraint identified by its code from the query.
removeDirectAttributesFromView(TemplateQuery) - Static method in class org.intermine.api.template.TemplateHelper
Removed from the view all the direct attributes that aren't editable constraints
removeEldestEntry(Map.Entry) - Method in class org.intermine.api.util.LimitedMap
 
removeFeature() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Remove the feature item that was set with setFeature() and associated synonyms
removeFieldDescriptor(Set<? extends FieldDescriptor>, String) - Static method in class org.intermine.modelproduction.ModelMerger
Remove a FieldDescriptor from a Set of FieldDescriptors by name.
removeFromBag(ObjectStoreBag, Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Removes an element from an ObjectStoreBag, delegate to internal ObjectStoreWriter.
removeFromBag(ObjectStoreBag, Integer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Removes an element from an ObjectStoreBag.
removeFromBag(ObjectStoreBag, Integer) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Removes an element from an ObjectStoreBag.
removeFromConstraintLogic(LogicExpression, String) - Static method in class org.intermine.api.query.MainHelper
Remove a constraint code from a logic expression, e.g.
removeFromView(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderViewChange
Remove a Node from the results view
removeIdFromBag(Integer) - Method in class org.intermine.api.profile.InterMineBag
Remove the given id from the bag, this updates the bag contents in the database
removeIdsFromBag(Collection<Integer>, boolean) - Method in class org.intermine.api.profile.InterMineBag
Remove the given ids from the bag, this updates the bag contents in the database
removeJob(String) - Method in class org.intermine.api.idresolution.IDResolver
 
removeNode(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Remove everything in a query under a given path.
removeObserver(WebSearchWatcher) - Method in class org.intermine.api.profile.StorableBag
 
removeObserver(WebSearchWatcher) - Method in interface org.intermine.api.search.WebSearchable
Remove this observer from the list of interested parties.
removeObserver(WebSearchWatcher) - Method in class org.intermine.api.template.ApiTemplate
 
removeOrderBy(String) - Method in class org.intermine.pathquery.PathQuery
Removes an element from the order by list of this query.
removePermanentToken(PermanentToken) - Method in class org.intermine.api.profile.ProfileManager
 
removeQuery(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Removes the current query from the session.
removeRedundancy(Map<String, ClassDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger
When changes are made to the inheritance hierarchy (especially the addition of superinterfaces), fields may be defined on superinterfaces making previous definitions further down the inheritance hierarchy redundant.
removeReference(String) - Method in class org.intermine.xml.full.Item
Remove a reference of the specified name if it exists.
removeSelectedFromBag(InterMineBag, HttpSession) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
remove the selected elements from the bag.
removeSequence(Connection, String) - Static method in class org.intermine.sql.DatabaseUtil
Remove the sequence from the database given.
removeSubclass(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Remove a subclass constraint from the query.
removeSubclassAndFixUp(String) - Method in class org.intermine.pathquery.PathQuery
Removes a subclass from the query, and removes any parts of the query that relied on it.
removeTags(String...) - Method in class org.intermine.webservice.client.lists.ItemList
Remove some tags from this list.
removeTags(ItemList, String...) - Method in class org.intermine.webservice.client.services.ListService
Get the tags for a list after removing some from its tag set.
removeTempBagTable(Connection, ObjectStoreInterMineImpl.BagTableToRemove) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Removes a temporary bag table, given a BagTableToRemove object.
removeToken(DeletionToken) - Method in class org.intermine.webservice.server.user.DeletionTokens
Remove this token.
removeTokensForProfile(Profile) - Method in class org.intermine.api.profile.ProfileManager
Remove auth tokens for a specified users.
removeVariable(String) - Method in class org.intermine.pathquery.LogicExpression
Remove a variable from the expression.
removeView(String) - Method in class org.intermine.pathquery.PathQuery
Removes a single element from the view list.
removeView(Connection, String) - Static method in class org.intermine.sql.DatabaseUtil
Remove the view from the database given.
rename(String) - Method in class org.intermine.api.profile.InvalidBag
Returns a new Invalid Bag identical to this one, but with the given name.
RENAME - Static variable in class org.intermine.api.profile.ModelUpdate
label in modelUpdate.properties file to identify renamed classes or fields
rename(String, String, String) - Method in class org.intermine.dwr.AjaxServices
Rename a element such as history, name, bag
rename(String) - Method in class org.intermine.webservice.client.lists.ItemList
Rename this list on the server.
rename(ItemList, String) - Method in class org.intermine.webservice.client.services.ListService
Rename a list on the server, returning a list representing the new state.
renameBag(String, String) - Method in class org.intermine.api.profile.Profile
Rename an existing bag, throw exceptions when bag doesn't exist of if new name already exists.
renameHistory(String, String) - Method in class org.intermine.api.profile.Profile
Rename an item in the history.
render(Object) - Static method in class org.intermine.objectstore.intermine.NotXmlRenderer
Render the given object as NotXml.
render(Collection<FastPathObject>, Model) - Static method in class org.intermine.xml.full.FullRenderer
Render a collection of objects as XML in InterMine Full format.
render(FastPathObject, Model) - Static method in class org.intermine.xml.full.FullRenderer
Render an Object as Xml in Full Data format.
render(Collection<Item>) - Static method in class org.intermine.xml.full.FullRenderer
Render a collection of items in InterMine Full XML format.
render(XMLStreamWriter, Item) - Static method in class org.intermine.xml.full.FullRenderer
Render the given Item as XML using an XMLStreamWriter
render(Item) - Static method in class org.intermine.xml.full.FullRenderer
Render the given Item as XML
RendererComparator - Class in org.intermine.xml.full
An implementation of Comparator to order pairs of Class objects.
RendererComparator() - Constructor for class org.intermine.xml.full.RendererComparator
 
renderImpl(XMLStreamWriter, Item) - Static method in class org.intermine.xml.full.FullRenderer
Render the given Item as XML using an XMLStreamWriter
reorder(String, String) - Method in class org.intermine.dwr.AjaxServices
AJAX request - reorder view.
reorderConstraints(String, String) - Method in class org.intermine.dwr.AjaxServices
AJAX request - reorder the constraints.
REPLACE_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
Whether to overwrite existing lists of the same name
replaceClob(Clob, String) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Replaces the contents of the given Clob with the given String.
replaceClob(Clob, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Replaces the contents of the given Clob with the given String.
replaceClob(Clob, String) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Replaces the contents of the given Clob with the given String.
replaceClobWithConnection(Connection, Clob, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Replaces the contents of the given Clob with the given String.
replaceConstraint(PathConstraint, PathConstraint) - Method in class org.intermine.pathquery.PathQuery
Replaces a constraint in the query with a different, carrying over the constraint code, and preserving the constraint logic.
replaceConstraint(PathConstraint, PathConstraint) - Method in class org.intermine.template.TemplateQuery
Replaces a constraint in the query with a different, carrying over the constraint code, and preserving the constraint logic.
replaceSpecialChars(String) - Static method in class org.intermine.api.util.NameUtil
Takes a string and replaces special characters with the text value, e.g. it would change "a&b" to "a_AMPERSAND_b".
replaceStrain(Integer) - Static method in class org.intermine.bio.util.BioUtil
Looks in the organism repo for the taxon ID provided.
REPORT_OBJECT_CACHE - Static variable in class org.intermine.web.logic.Constants
The session attribute that holds the ReportObjectCache object for the session.
REPORT_TEMPLATE - Static variable in class org.intermine.api.config.Constants
checks for object in other mine
ReportAspectController - Class in org.intermine.web.struts
Controller for the reportAspect tile.
ReportAspectController() - Constructor for class org.intermine.web.struts.ReportAspectController
 
ReportController - Class in org.intermine.web.struts
New objectDetails.
ReportController() - Constructor for class org.intermine.web.struts.ReportController
 
ReportDisplayer - Class in org.intermine.web.displayer
Parent class for report displayers that appear on report pages.
ReportDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.web.displayer.ReportDisplayer
Construct with config information read from webconfig-model.xml and the API.
ReportDisplayerConfig - Class in org.intermine.web.logic.config
Bean to hold configuration for report displayers.
ReportDisplayerConfig() - Constructor for class org.intermine.web.logic.config.ReportDisplayerConfig
 
ReportDisplayerController - Class in org.intermine.web.struts
Execute a ReportDisplayer placed on the context.
ReportDisplayerController() - Constructor for class org.intermine.web.struts.ReportDisplayerController
 
reportDone(PrefetchManager.Request) - Static method in class org.intermine.objectstore.query.PrefetchManager
Allows a system to report that it has finished servicing a particular request.
ReportInList - Class in org.intermine.web.logic.results
Wrapper, mainly to provide size
ReportInList(Collection<InterMineBag>) - Constructor for class org.intermine.web.logic.results.ReportInList
Setup
ReportInListController - Class in org.intermine.web.struts
 
ReportInListController() - Constructor for class org.intermine.web.struts.ReportInListController
 
ReportObject - Class in org.intermine.web.logic.results
Object to be displayed on report.do
ReportObject(InterMineObject, WebConfig, InterMineAPI, Properties) - Constructor for class org.intermine.web.logic.results.ReportObject
Setup internal ReportObject
ReportObject.TitleValue - Class in org.intermine.web.logic.results
Holder for formatted and unformatted versions of a title part.
ReportObjectFactory - Class in org.intermine.web.logic.results
A factory for ReportObjects.
ReportObjectFactory(InterMineAPI, WebConfig, Properties) - Constructor for class org.intermine.web.logic.results.ReportObjectFactory
Create a new ReportObjectCache for the given session.
ReportObjectField - Class in org.intermine.web.logic.results
Object field, used in header the summary of ReportObject
ReportObjectField(String, String, Object, String, boolean, boolean) - Constructor for class org.intermine.web.logic.results.ReportObjectField
Constructor
ReportObjectField(String, String, Object, String, boolean, boolean, String) - Constructor for class org.intermine.web.logic.results.ReportObjectField
Constructor
ReportTemplateController - Class in org.intermine.web.struts
Controller for an inline table created by running a template on a report page.
ReportTemplateController() - Constructor for class org.intermine.web.struts.ReportTemplateController
 
ReportWidgetDisplayer - Class in org.intermine.bio.web.displayer
 
ReportWidgetDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.ReportWidgetDisplayer
 
Request - Interface in org.intermine.webservice.client.core
Client request interface.
request - Variable in class org.intermine.webservice.server.lists.ListInput
 
request - Variable in class org.intermine.webservice.server.query.QueryRequestParser
 
request - Variable in class org.intermine.webservice.server.WebService
The servlet request.
Request.RequestType - Enum in org.intermine.webservice.client.core
 
RequestImpl - Class in org.intermine.webservice.client.core
Implementation of Request interface.
RequestImpl(Request.RequestType, String, ContentType) - Constructor for class org.intermine.webservice.client.core.RequestImpl
Constructor.
requestIsOfSuitableType() - Method in class org.intermine.webservice.server.lists.ListUploadService
Determine if we should service this request.
RequestPasswordAction - Class in org.intermine.web.struts
Action to handle button presses RequestPasswordForm
RequestPasswordAction() - Constructor for class org.intermine.web.struts.RequestPasswordAction
 
RequestPasswordForm - Class in org.intermine.web.struts
Form used to request a password
RequestPasswordForm() - Constructor for class org.intermine.web.struts.RequestPasswordForm
 
RequestSubClassFilter - Class in org.intermine.webservice.server.filter
Filter to wrap all web service requests in a custom delegating wrapper that prevents sessions being created.
RequestSubClassFilter() - Constructor for class org.intermine.webservice.server.filter.RequestSubClassFilter
 
requestURL(String, ContentType) - Method in class org.intermine.api.mines.HttpRequester
 
requestURL(String, ContentType) - Method in interface org.intermine.api.mines.MineRequester
Request information as encoded in a string.
RequestUtil - Class in org.intermine.web.logic
Util methods for HttpServletRequest.
RESERVED_KEYS - Static variable in class org.intermine.webservice.server.output.JSONFormatter
keys which you aren't allowed to set.
reset() - Static method in class org.intermine.api.query.MainHelper.RangeConfig
reset
reset() - Method in class org.intermine.bio.dataconversion.UniprotEntry
this temporary variable is set whilst we are processing items that span multiple XML tags.
reset() - Static method in class org.intermine.bio.ontology.SequenceOntologyFactory
Remove instance, used for testing only
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.bio.web.struts.SequenceExportForm
Reset the form to the initial state
reset() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Resets the IntegrationWriter, clearing the id map and the hints
reset() - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Resets the IntegrationWriter, clearing the id map and the hints
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.BagUploadConfirmForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.BuildBagForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ChangePasswordForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ChangeTableSizeForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ContactForm
Reset form bean.
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.CreateAccountForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.EditPropertiesForm
 
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.FindInListForm
Reset form bean.
reset() - Method in class org.intermine.web.struts.ImportQueriesForm
Reset the form.
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ImportTagsForm
reset() - Method in class org.intermine.web.struts.ImportTagsForm
Reset the form.
reset() - Method in class org.intermine.web.struts.ImportXMLForm
Reset the form.
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ImportXMLForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.InvitationForm
 
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.LoginForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyBagForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyQueryForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifySuperUserForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyTemplateForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.PasswordResetForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.QueryForm
 
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.RequestPasswordForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.SaveBagForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.SaveQueryForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.TableExportForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.TemplateForm
reset() - Method in class org.intermine.web.struts.TemplateForm
Reset the form
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.TemplateSettingsForm
Reset the form bean taking initial state from current TemplateBuildState session attribute.
reset() - Method in class org.intermine.web.struts.TemplatesImportForm
Reset the form.
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.WidgetForm
ResidueFieldExporter - Class in org.intermine.bio.web.export
ResidueFieldExporter class
ResidueFieldExporter() - Constructor for class org.intermine.bio.web.export.ResidueFieldExporter
 
ResolutionJob - Class in org.intermine.api.idresolution
 
ResolutionJob(UUID, BagQueryRunner, JobInput) - Constructor for class org.intermine.api.idresolution.ResolutionJob
 
resolveCollectionPath(Path, Object) - Static method in class org.intermine.api.util.PathUtil
Return the object at the end of a given path, starting from the given object.
resolvedIdentifier - Variable in class org.intermine.bio.dataconversion.TreefamConverter.GeneHolder
 
resolveId(String, String) - Method in class org.intermine.bio.dataconversion.DoNothingIdResolver
 
resolveId(String, String, String) - Method in class org.intermine.bio.dataconversion.IdResolver
For the given id return a set of matching primary identifiers in the given taxonId.
resolveId(String, String) - Method in class org.intermine.bio.dataconversion.IdResolver
For the given id return a set of matching primary identifiers in the given taxonId.
resolveIds(String, String, List<String>) - Method in class org.intermine.bio.dataconversion.IdResolver
For the given set of ids return a map of matching primary identifiers in the given taxonId.
resolveIds(String, List<String>) - Method in class org.intermine.bio.dataconversion.IdResolver
For the given id set return a map of matching primary identifiers in the given taxonId.
resolveInvitation(SharingInvite, Profile, boolean) - Method in class org.intermine.api.bag.SharedBagManager
Either reject or accept an invitation to share a list.
resolvePath(Path, Object) - Static method in class org.intermine.api.util.PathUtil
Return the object at the end of a given path, starting from the given object.
resolver - Static variable in class org.intermine.bio.dataconversion.IdResolverFactory
 
resolveValue(FastPathObject, String) - Static method in class org.intermine.webservice.server.jbrowse.Queries
 
ResourceFinder - Class in org.intermine.web.struts
A class for finding resources in the WEB-INF directory at run-time based on patterns.
ResourceFinder(ServletContext) - Constructor for class org.intermine.web.struts.ResourceFinder
Constructor.
ResourceNotFoundException - Exception in org.intermine.webservice.client.exceptions
The ResourceNotFoundException is thrown by a service provider when an attempt is made to perform an operation upon a resource that cannot be found.
ResourceNotFoundException(String) - Constructor for exception org.intermine.webservice.client.exceptions.ResourceNotFoundException
 
ResourceNotFoundException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ResourceNotFoundException
 
ResourceNotFoundException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ResourceNotFoundException
 
ResourceNotFoundException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.ResourceNotFoundException
 
ResourceNotFoundException - Exception in org.intermine.webservice.server.exceptions
The ResourceNotFoundException is thrown by a service provider when an attempt is made to perform an operation upon a resource that cannot be found.
ResourceNotFoundException(String) - Constructor for exception org.intermine.webservice.server.exceptions.ResourceNotFoundException
 
ResourceNotFoundException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ResourceNotFoundException
 
ResourceNotFoundException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ResourceNotFoundException
 
ResourceOpener - Interface in org.intermine.web.logic
The type of objects that can open resources by names.
resourceUrl - Variable in class org.intermine.webservice.client.core.Service
 
respond(WebServiceServlet.Method, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.core.WebServiceServlet
Respond to a request.
respond(WebServiceServlet.Method, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.idresolution.IdResolutionServlet
 
respond(WebServiceServlet.Method, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.user.DeregistrationTokenServlet
 
respond(WebServiceServlet.Method, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.user.PermaTokensServlet
 
response - Variable in class org.intermine.webservice.server.WebService
The servlet response.
ResponseType - Enum in org.intermine.web.struts.oauth2
 
ResponseUtil - Class in org.intermine.web.logic.export
Response util that sets content type and header for various formats and has util methods for setting headers controlling cache.
RestfulServlet - Class in org.intermine.webservice.server.core
 
RestfulServlet() - Constructor for class org.intermine.webservice.server.core.RestfulServlet
 
restoreFromFile(Set<String>) - Method in class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory
Populate the ID resolver from a cached file
restoreFromFile(File) - Method in class org.intermine.bio.dataconversion.IdResolverFactory
Read IdResolver contents from a file, allows for caching during build.
restoreFromFile() - Method in class org.intermine.bio.dataconversion.IdResolverFactory
Read IdResolver contents from a file, allows for caching during build.
ResultCell - Interface in org.intermine.api.results
An interface for result cells
ResultElement - Class in org.intermine.api.results
Cell of results table containing information for the parent Object
ResultElement(FastPathObject, Path, boolean) - Constructor for class org.intermine.api.results.ResultElement
Constructs a new ResultCell object
ResultElement(Object) - Constructor for class org.intermine.api.results.ResultElement
Create a ResultElement that displays a single raw value.
ResultElementConverter - Class in org.intermine.web.logic.export
 
ResultElementConverter() - Constructor for class org.intermine.web.logic.export.ResultElementConverter
 
ResultException - Exception in org.intermine.webservice.client.exceptions
ResultException is the exception thrown when a request fails.
ResultException(String) - Constructor for exception org.intermine.webservice.client.exceptions.ResultException
 
ResultException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ResultException
 
ResultException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ResultException
 
ResultException(String, String) - Constructor for exception org.intermine.webservice.client.exceptions.ResultException
Construct an informative exception.
ResultProcessor - Class in org.intermine.webservice.server.core
Processor of Results object for easy accessing and parsing of results to list of strings.
ResultProcessor() - Constructor for class org.intermine.webservice.server.core.ResultProcessor
Constructor.
ResultRowList - Class in org.intermine.webservice.client.results
A representation of a result row that allows parsed objects to be retrieved by index, where the order of elements is the same as that of the view list of the originating PathQuery.
ResultRowList(JSONArray) - Constructor for class org.intermine.webservice.client.results.ResultRowList
Construct a new result row object backed by the given JSONArray.
ResultRowList(String) - Constructor for class org.intermine.webservice.client.results.ResultRowList
Construct a new result row object backed by the JSONArray which can be parsed from the given String.
ResultRowMap - Class in org.intermine.webservice.client.results
A class that represents a row of a result set as a map from column names to values.
ResultRowMap(JSONArray, List<String>) - Constructor for class org.intermine.webservice.client.results.ResultRowMap
Construct a result-row with a JSONArray as its backing data store.
ResultRowMap(String, List<String>) - Constructor for class org.intermine.webservice.client.results.ResultRowMap
Construct a result-row with a String as its backing data store.
ResultRowParser - Interface in org.intermine.webservice.server.core
Interface of parser that parses row of results to list of strings.
results - Variable in class org.intermine.api.results.ExportResultsIterator
 
results - Variable in class org.intermine.objectstore.query.ClobAccess
 
Results - Class in org.intermine.objectstore.query
Results representation as a List of ResultRows.
Results() - Constructor for class org.intermine.objectstore.query.Results
No argument constructor for testing purposes
Results(Query, ObjectStore, Map<Object, Integer>) - Constructor for class org.intermine.objectstore.query.Results
Constructor for a Results object.
Results(ResultsBatches, boolean, boolean, boolean) - Constructor for class org.intermine.objectstore.query.Results
Constructor for a Results object, given a ResultsBatches object.
results - Variable in class org.intermine.web.logic.results.InlineResultsTable
 
results(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoadTemplateAction
Load a template from template name passed as parameter.
RESULTS_TABLE_SIZE - Static variable in class org.intermine.web.logic.Constants
Session attribute used to store the size of table with results.
ResultsAction - Class in org.intermine.web.struts
ResultsAction is called before results table is rendered.
ResultsAction() - Constructor for class org.intermine.web.struts.ResultsAction
 
resultsAsList - Variable in class org.intermine.web.logic.results.InlineResultsTable
 
resultsBatches - Variable in class org.intermine.objectstore.query.Results
 
ResultsBatches - Class in org.intermine.objectstore.query
Class holding the data batches for the Results object.
ResultsBatches(Query, ObjectStore, Map<Object, Integer>) - Constructor for class org.intermine.objectstore.query.ResultsBatches
Construct a new ResultsBatches object.
resultsCache - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
ResultsConverter - Class in org.intermine.objectstore.intermine
Provides a method to convert from SQL ResultSet data to InterMine object-based data.
ResultSet - Class in org.intermine.webservice.client.results
Common behaviour and interface for result sets.
ResultSet(HttpConnection) - Constructor for class org.intermine.webservice.client.results.ResultSet
Constructor.
ResultSet(String) - Constructor for class org.intermine.webservice.client.results.ResultSet
Constructor with a String.
ResultSet(BufferedReader) - Constructor for class org.intermine.webservice.client.results.ResultSet
Constructor with a reader.
ResultsFlatOuterJoinsImpl - Class in org.intermine.api.results.flatouterjoins
Provides an implementation of List that encapsulates another List (like a Results object), and translates row into flat MultiRow format in a way suitable for displaying in the webapp.
ResultsFlatOuterJoinsImpl(List<ResultsRow>, Query) - Constructor for class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
Constructor for this object.
ResultsInfo - Class in org.intermine.objectstore.query
Represents a result from the estimate() method of an ObjectStore.
ResultsInfo() - Constructor for class org.intermine.objectstore.query.ResultsInfo
No-arg constructor to allow serialization
ResultsInfo(long, long, int) - Constructor for class org.intermine.objectstore.query.ResultsInfo
Constructs an instance of ResultsInfo with all new parameters, without min and max.
ResultsInfo(long, long, int, int, int) - Constructor for class org.intermine.objectstore.query.ResultsInfo
Constructs an instance of ResultsInfo with all new parameters.
ResultsInfo(ResultsInfo, int, int) - Constructor for class org.intermine.objectstore.query.ResultsInfo
Constructs an instance of ResultsInfo from another ResultsInfo and a new min and max.
ResultsRow<E> - Class in org.intermine.objectstore.query
 
ResultsRow() - Constructor for class org.intermine.objectstore.query.ResultsRow
 
ResultsRow(Collection<? extends E>) - Constructor for class org.intermine.objectstore.query.ResultsRow
 
ResultsWithFacets - Class in org.intermine.api.lucene
A class that wraps both a collection of hits and a collection of facets.
ResultsWithFacets(Collection<KeywordSearchHit>, Collection<KeywordSearchFacet>, int) - Constructor for class org.intermine.api.lucene.ResultsWithFacets
 
retainAll(Collection<?>) - Method in class org.intermine.util.PseudoSet
retainAll(Collection<?>) - Method in class org.intermine.webservice.client.results.ResultRowList
 
retrieve(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager
Retrieve the value for a given key from the metadata table of the database
retrieveBag(String) - Method in class org.intermine.webservice.server.widget.WidgetService
Get the bag in question.
retrieveBLOBInputStream(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager
Retrieve the BLOB value for a given key from the metadata table of the database
retrieveExplainString(Statement) - Method in class org.intermine.sql.query.PostgresExplainResult
Retrieve EXPLAIN String from post-7.3 databases
RetrieveMetadataTask - Class in org.intermine.task
Retrieve the model metadata from a database
RetrieveMetadataTask() - Constructor for class org.intermine.task.RetrieveMetadataTask
 
retrieveToken(UUID) - Method in class org.intermine.webservice.server.user.DeletionTokens
Retrieve a token by its identifier.
returnNewTableRow() - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable
Create a table row object
returnNewTableRow() - Method in class org.intermine.web.logic.results.InlineResultsTable
Create a table row object, overriden on BagUploadConfirm where we go custom
returnToString - Variable in class org.intermine.web.struts.LoginForm
 
reverseCapitalisation(String) - Static method in class org.intermine.metadata.StringUtil
Reverses the capitalisation of the first character of the given String.
reverseEvaluate(Integer) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.StainingLevelEvaluator
Integer value to string conversion
reverseRefDesc - Variable in class org.intermine.metadata.ReferenceDescriptor
 
reverseRefName - Variable in class org.intermine.metadata.ReferenceDescriptor
 
RgdIdentifiersResolverFactory - Class in org.intermine.bio.dataconversion
ID resolver for RGD genes.
RgdIdentifiersResolverFactory() - Constructor for class org.intermine.bio.dataconversion.RgdIdentifiersResolverFactory
Construct with SO term of the feature type.
RgdIdentifiersResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.RgdIdentifiersResolverFactory
Construct with SO term of the feature type.
right - Variable in class org.intermine.objectstore.query.OverlapConstraint
 
right - Variable in class org.intermine.sql.query.Constraint
 
right - Variable in class org.intermine.sql.query.InListConstraint
 
right - Variable in class org.intermine.sql.query.SubQueryConstraint
 
RIGHT_BRACE - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
RIGHT_FALSE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints, where the right is always false.
RIGHT_TRUE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints, where the right is always true.
RNAiDisplayer - Class in org.flymine.web.displayer
Displayer for fly rnai data
RNAiDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.flymine.web.displayer.RNAiDisplayer
 
ROUND - Static variable in class org.intermine.objectstore.query.QueryFunction
Round to a given number of decimal places.
Row - Class in org.intermine.sql.writebatch
Stores two ints.
Row(int, int) - Constructor for class org.intermine.sql.writebatch.Row
Constructor.
ROW_SEPARATOR - Static variable in class org.intermine.metadata.TextTable
An object representing a horizontal line separating two rows - treated as a row.
RowFormatter - Interface in org.intermine.web.logic.export
Interface denoting that object is able format list of objects to string.
RowFormatterImpl - Class in org.intermine.web.logic.export
Implements RowFormatter interface.
RowFormatterImpl(String, boolean) - Constructor for class org.intermine.web.logic.export.RowFormatterImpl
Constructor.
rowObjects - Variable in class org.intermine.web.logic.results.InlineResultsTable
 
RowResultSet - Class in org.intermine.webservice.client.results
A class for managing results received as a jsonrows result-set.
RowResultSet(HttpConnection, List<String>, int) - Constructor for class org.intermine.webservice.client.results.RowResultSet
Construct a new result-set with an HttpConnection and a list of output columns.
RowResultSet(BufferedReader, List<String>, int) - Constructor for class org.intermine.webservice.client.results.RowResultSet
Constructor with a reader.
RowResultSet(String, List<String>) - Constructor for class org.intermine.webservice.client.results.RowResultSet
Construct a new result-set from a string and a list of output columns.
rows - Variable in class org.intermine.objectstore.query.ResultsInfo
 
rows - Variable in class org.intermine.sql.query.ExplainResult
 
rslv - Variable in class org.intermine.bio.dataconversion.BioGridConverter
 
rslv - Variable in class org.intermine.bio.dataconversion.EnsemblComparaConverter
 
rslv - Variable in class org.intermine.bio.dataconversion.GoConverter
 
rslv - Variable in class org.intermine.bio.dataconversion.KeggOrthologuesConverter
 
rslv - Variable in class org.intermine.bio.dataconversion.KeggPathwayConverter
 
rslv - Variable in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
 
rslv - Variable in class org.intermine.bio.dataconversion.OrthodbConverter
 
rslv - Variable in class org.intermine.bio.dataconversion.PsiConverter
 
rslv - Variable in class org.intermine.bio.dataconversion.PubMedGeneConverter
 
rslv - Variable in class org.intermine.bio.dataconversion.TreefamConverter
 
rslv - Variable in class org.intermine.bio.dataconversion.UniprotConverter
 
run() - Method in interface org.intermine.api.idresolution.Job
run job
run() - Method in class org.intermine.api.idresolution.ResolutionJob
 
run() - Method in class org.intermine.api.idresolution.UpgradeJob
 
run() - Method in class org.intermine.api.lucene.InterMineObjectFetcher
fetch objects from database, create documents and add them to the queue
run() - Method in class org.intermine.api.tracker.TrackerLogger
run() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner
 
run(PreparedStatement) - Method in class org.intermine.objectstore.intermine.SQLOperation
The code that the operation represents.
run() - Method in class org.intermine.util.ShutdownHook
 
run() - Method in class org.intermine.web.context.MailDaemon
 
run() - Method in class org.intermine.web.logic.profile.UpgradeBagList
 
run(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryChangeAction
Excecute a query.
run() - Method in class org.intermine.web.struts.Registrar
Send a post request to the registry service, if one has been set up.
run() - Method in class org.intermine.webservice.server.idresolution.JobJanitor
 
run(Command) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
runAllTests(Database, LineNumberReader) - Method in class org.intermine.task.AcceptanceTestTask
Run all the tests and return a List of AcceptanceTestResult objects.
runBagUpgrade(UpgradeBagList, InterMineAPI, Profile) - Static method in class org.intermine.web.logic.profile.LoginHandler
Kick off a bag upgrade for current user.
runBrowseSearch(String, int, Map<String, String>, List<Integer>, int) - Static method in class org.intermine.api.lucene.KeywordSearch
perform a keyword search using bobo-browse for faceting and pagination
runBrowseSearch(String, int, Map<String, String>, List<Integer>, boolean, int) - Static method in class org.intermine.api.lucene.KeywordSearch
perform a keyword search using bobo-browse for faceting and pagination
runBrowseWithFacets(InterMineAPI, String, int, Map<String, String>, List<Integer>) - Static method in class org.intermine.api.lucene.KeywordSearch
Run a browse search and get back both search results and facet information.
RunIqlQueryTask - Class in org.intermine.task
Ant task to read an IQL query from a -Dquery="QUERY" parameter and execute it in the database.
RunIqlQueryTask() - Constructor for class org.intermine.task.RunIqlQueryTask
 
runLuceneSearch(String) - Static method in class org.intermine.api.lucene.KeywordSearch
Deprecated.
Use runBrowseSearch instead.
runLuceneSearch(String, SearchTarget, SearchRepository) - Static method in class org.intermine.api.search.SearchResults
Search a Lucene index and return a search result.
RUNNING_QUERIES - Static variable in class org.intermine.web.logic.Constants
Session attribute.
runPathQuery(PathQuery, int, int) - Method in class org.intermine.webservice.server.query.result.QueryResultService
Runs path query and returns to output obtained results.
runPathQuery(PathQuery, int, int) - Method in class org.intermine.webservice.server.query.result.TableRowService
 
runQuery(HttpSession, MessageResources, String, SessionMethods.Action, SessionMethods.CompletionCallBack) - Static method in class org.intermine.web.logic.session.SessionMethods
Executes an action and call a callback when it completes successfully.
RunQueryAction - Class in org.intermine.web.struts
Run a query as passed in directly as XML.
RunQueryAction() - Constructor for class org.intermine.web.struts.RunQueryAction
 
runTemplate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails
Show in table for inline template queries.

S

SAFENESS_ANTISAFE - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
Safeness value indicating a situation safe for ContainsConstraint DOES NOT CONTAIN
SAFENESS_SAFE - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
Safeness value indicating a situation safe for ContainsConstraint CONTAINS
SAFENESS_UNSAFE - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
Safeness value indicating a situation unsafe for ContainsConstraint
save() - Method in class org.intermine.api.bag.SharingInvite
 
save(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryChangeAction
Save a query from the history.
saveBag(InterMineBag) - Method in class org.intermine.api.profile.Profile
Stores a new bag in the profile.
saveBag(String, InterMineBag) - Method in class org.intermine.api.profile.Profile
Stores a new bag in the profile.
saveBag(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SaveBagAction
Save the selected objects to a bag on the session
SaveBagAction - Class in org.intermine.web.struts
Saves selected items in a new bag or combines with existing bag.
SaveBagAction() - Constructor for class org.intermine.web.struts.SaveBagAction
 
saveBagDescription(String, String) - Method in class org.intermine.dwr.AjaxServices
For a given bag, set its description
SaveBagForm - Class in org.intermine.web.struts
Form bean for the results table and bag creation form.
SaveBagForm() - Constructor for class org.intermine.web.struts.SaveBagForm
Constructor
saveClassKeys(String, File) - Static method in class org.intermine.modelproduction.MetadataManager
Save the class keys, in serialized form, to the specified directory
SAVED_BAG_STATUS - Static variable in class org.intermine.web.logic.Constants
key for the map saved in the session containing the status of saved bags
savedBagId - Variable in class org.intermine.api.profile.StorableBag
 
savedBags - Variable in class org.intermine.api.profile.Profile
 
savedCounts - Variable in class org.intermine.dataloader.HintingFetcher
 
savedInvalidBags - Variable in class org.intermine.api.profile.Profile
 
savedQueries - Variable in class org.intermine.api.profile.Profile
 
SavedQuery - Class in org.intermine.api.profile
Container for a saved query.
SavedQuery(String, Date, PathQuery) - Constructor for class org.intermine.api.profile.SavedQuery
Construct a new instance of SavedQuery.
SavedQueryBinding - Class in org.intermine.api.xml
Convert SavedQuerys to and from XML
SavedQueryHandler - Class in org.intermine.api.xml
Extension of PathQueryHandler to handle parsing SavedQuerys
SavedQueryHandler(Map<String, SavedQuery>, Map, int) - Constructor for class org.intermine.api.xml.SavedQueryHandler
Constructor
SavedQueryRetrievalService - Class in org.intermine.webservice.server.query
 
SavedQueryRetrievalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.SavedQueryRetrievalService
 
savedTemplateQuery - Variable in class org.intermine.api.template.ApiTemplate
SavedTemplateQuery object in the UserProfile database, so we can update summaries.
savedTemplates - Variable in class org.intermine.api.profile.Profile
 
savedTimes - Variable in class org.intermine.dataloader.HintingFetcher
 
SaveFromIdsToBagAction - Class in org.intermine.web.struts
Saves selected items with InterMine ids and a Type in a new bag or combines with existing bag.
SaveFromIdsToBagAction() - Constructor for class org.intermine.web.struts.SaveFromIdsToBagAction
 
saveHistory(SavedQuery) - Method in class org.intermine.api.profile.Profile
Save a query to the query history.
saveIndexToDatabase(ObjectStore, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.lucene.KeywordSearch
writes index and associated directory to the database using the metadatamanager.
saveKeyDefinitions(String, File, String) - Static method in class org.intermine.modelproduction.MetadataManager
Save the key definitions, in serialized form, to the specified directory
saveModel(Model, File) - Static method in class org.intermine.modelproduction.MetadataManager
Save a model, in serialized form, to the specified directory
saveObjectIdOnTableRow(Integer, Object) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable
Set InterMine Object id for the table row
saveObjectIdOnTableRow(Integer, Object) - Method in class org.intermine.web.logic.results.InlineResultsTable
Used on BagUploadConfirm
savePopulation - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
saveProfile(Profile) - Method in class org.intermine.api.profile.ProfileManager
Synchronise a user's Profile with the backing store
saveProperties(String, File, String) - Static method in class org.intermine.modelproduction.MetadataManager
Save the objectstore summary, in serialized form, to the specified directory
saveQueries(Map<? extends String, ? extends PathQuery>) - Method in class org.intermine.api.profile.Profile
Save the map of queries as given to the user's profile, avoiding all possible name collisions.
saveQueries(Map<String, PathQuery>) - Method in class org.intermine.webservice.server.query.QueryUpdateService
 
saveQueries(Map<String, PathQuery>) - Method in class org.intermine.webservice.server.query.QueryUploadService
Save the given queries.
saveQuery(String, SavedQuery) - Method in class org.intermine.api.profile.Profile
Save or update a query.
saveQuery(HttpSession, String, PathQuery, Date) - Static method in class org.intermine.web.logic.session.SessionMethods
Save a clone of a query to the user's Profile.
saveQuery(HttpSession, String, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods
Save a clone of a query to the user's Profile.
SaveQueryAction - Class in org.intermine.web.struts
Implementation of Action that saves a Query from a session.
SaveQueryAction() - Constructor for class org.intermine.web.struts.SaveQueryAction
 
SaveQueryForm - Class in org.intermine.web.struts
Form bean to represent the inputs to the query saving action
SaveQueryForm() - Constructor for class org.intermine.web.struts.SaveQueryForm
 
saveQueryToHistory(HttpSession, String, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods
Save a clone of a query to the user's Profile history.
saveTemplate(String, ApiTemplate) - Method in class org.intermine.api.profile.Profile
Save a template
saveToggleState(String, boolean) - Static method in class org.intermine.dwr.AjaxServices
Saves information, that some element was toggled - displayed or hidden.
saveWithBagValues(Integer, Collection<BagValue>) - Method in class org.intermine.api.profile.StorableBag
Save the bag into the userprofile database, along with information about what kinds of values this bag contains.
savingDisabled - Variable in class org.intermine.api.profile.Profile
 
SAXParser - Class in org.intermine.metadata
Basic SAX Parser
SAXParser - Class in org.intermine.util
Basic SAX Parser
sb - Variable in class org.intermine.sql.logging.DatabaseWriter
 
SC_BAD_REQUEST - Static variable in class org.intermine.webservice.server.output.Output
Bad request http status code.
SC_FORBIDDEN - Static variable in class org.intermine.webservice.server.output.Output
Forbidden http status code.
SC_INTERNAL_SERVER_ERROR - Static variable in class org.intermine.webservice.server.output.Output
Internal server http status code.
SC_NO_CONTENT - Static variable in class org.intermine.webservice.server.output.Output
No content http status code.
SC_NOT_FOUND - Static variable in class org.intermine.webservice.server.output.Output
Resource not found http status code.
SC_OK - Static variable in class org.intermine.webservice.server.output.Output
OK http status code.
SC_UNAUTHORIZED - Static variable in class org.intermine.webservice.server.output.Output
Request is legal, but requires authentication, which was either not provided, or failed.
schema - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
schema - Variable in class org.intermine.objectstore.intermine.TorqueModelOutput
 
schema - Variable in class org.intermine.objectstore.intermine.TorqueModelOutputTask
 
schemaFile - Variable in class org.intermine.task.BuildDbTask
 
SchemaListService - Class in org.intermine.webservice.server
Serve up the list of schemata that we have.
SchemaListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.SchemaListService
Constructor
SchemaServlet - Class in org.intermine.webservice.server
Returns a requested schema.
SchemaServlet() - Constructor for class org.intermine.webservice.server.SchemaServlet
 
Scope - Class in org.intermine.api.search
Scope constants.
SCOPES - Static variable in class org.intermine.api.search.Scope
The possible scopes.
score(int) - Method in class org.intermine.sql.precompute.OptimiserCacheLine
Scores this cache line according to how far away the required limit is from the limit used to create the line.
search(String, Collection<String>, String, boolean, boolean) - Method in class org.intermine.api.bag.BagQueryRunner
Given an input list of string identifiers search for corresponding objects.
search() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner
Main body of db search
SEARCH_INDEX - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key to use to store the search index.
SEARCH_INDEX_DIRECTORY - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key to use to store the search Directory.
SEARCH_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of class that tracks searches
SEARCH_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of table that tracks searches
SearchFilterEngine - Class in org.intermine.api.search
Class filtering web searchables according to the associated tags.
SearchFilterEngine() - Constructor for class org.intermine.api.search.SearchFilterEngine
 
searchForBag(String, List<String>, String, boolean) - Method in class org.intermine.api.bag.BagQueryRunner
Given an input list of string identifiers search for corresponding objects.
searchItems - Variable in class org.intermine.api.search.SearchRepository
 
SearchRepository - Class in org.intermine.api.search
The base class for search repositories.
SearchRepository(Profile) - Constructor for class org.intermine.api.search.SearchRepository
Constructor.
SearchResult - Class in org.intermine.api.search
A single item in a set or returned results formed by searching the web-searchable indices with Lucene.
SearchResults - Class in org.intermine.api.search
Representations of Lucene search results over the web-searchable data of the user-profile and the mechanisms for generating a set of such results.
SearchTarget - Class in org.intermine.api.search
An object for encapsulating the scope and type of object requested from a Lucene search of the user profile web searchable items.
SearchTarget(String, String) - Constructor for class org.intermine.api.search.SearchTarget
Constructor.
SEARCHTRACK - Static variable in class org.intermine.api.tracker.xml.SearchTrackBinding
label for XML
SearchTrackBinding - Class in org.intermine.api.tracker.xml
 
SEARCHTRACKS - Static variable in class org.intermine.api.tracker.xml.SearchTrackBinding
label for XML
SearchUtils - Class in org.intermine.web.search
The bits of the search infrastructure that belong in the web-package because they have view dependent logic.
seenBrokenOneToMany - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
Segment - Class in org.intermine.webservice.server.jbrowse
Represents an interbase segment.
select - Variable in class org.intermine.sql.query.Query
 
select(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TreeAction
Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
selectable - Variable in class org.intermine.api.results.Column
 
selectAll(int, String) - Static method in class org.intermine.dwr.AjaxServices
Select all the elements in a PagedTable
selected - Variable in class org.intermine.web.struts.ModifyTemplateForm
 
selectedBags - Variable in class org.intermine.web.struts.ModifyBagForm
 
selectedElements - Variable in class org.intermine.web.struts.ModifyBagDetailsForm
 
selectedIdsIterator() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return an Iterator over the selected Ids
selectedObjects - Variable in class org.intermine.web.struts.SaveBagForm
 
selectedQueries - Variable in class org.intermine.web.struts.ModifyQueryForm
 
selectEncoding(ServletRequest) - Method in class org.intermine.web.filters.SetCharacterEncodingFilter
Select an appropriate character encoding to be used, based on the characteristics of the current request and/or filter initialization parameters.
selectId(String, String, String) - Static method in class org.intermine.dwr.AjaxServices
Add an ID to the PagedTable selection
selectId(Integer, int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Add an object id and its field value that has been selected in the table.
SelectValue - Class in org.intermine.sql.query
Represents an AbstractValue with an alias, suitable for use in the SELECT portion of an SQL query.
SelectValue(AbstractValue, String) - Constructor for class org.intermine.sql.query.SelectValue
Construct a new SelectValue.
sendFareWell(String, String) - Method in class org.intermine.util.Emailer
Bid a user farewell from the system.
SensibleByteArrayOutputStream - Class in org.intermine.util
A subclass of ByteArrayOutputStream that behaves a little more sensibly when handling large writes followed by small writes.
SensibleByteArrayOutputStream() - Constructor for class org.intermine.util.SensibleByteArrayOutputStream
 
SensibleByteArrayOutputStream(int) - Constructor for class org.intermine.util.SensibleByteArrayOutputStream
 
SEPARATOR - Static variable in class org.intermine.api.tag.TagNames
Tag separator.
seqClsName - Variable in class org.intermine.bio.task.GFF3ConverterTask
 
seqDataSourceName - Variable in class org.intermine.bio.task.GFF3ConverterTask
 
sequence - Variable in class org.intermine.objectstore.query.ResultsBatches
 
SEQUENCE_IGNORE - Static variable in interface org.intermine.objectstore.ObjectStore
Object representing no fail-fast concurrency checks required.
SEQUENCE_MULTIPLE - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
sequenceBase - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
SequenceExportAction - Class in org.intermine.bio.web.struts
Exports sequence.
SequenceExportAction() - Constructor for class org.intermine.bio.web.struts.SequenceExportAction
 
SequenceExporter - Class in org.intermine.bio.web.export
Export data in FASTA format.
SequenceExporter(ObjectStore, OutputStream, int, Map<String, List<FieldDescriptor>>, int) - Constructor for class org.intermine.bio.web.export.SequenceExporter
Constructor.
SequenceExporter(ObjectStore, OutputStream, int, Map<String, List<FieldDescriptor>>, int, List<Path>) - Constructor for class org.intermine.bio.web.export.SequenceExporter
Constructor.
SequenceExportForm - Class in org.intermine.bio.web.struts
Form for sequence export (FASTA etc.)
SequenceExportForm() - Constructor for class org.intermine.bio.web.struts.SequenceExportForm
Constructor
SequenceExportOptionsController - Class in org.intermine.bio.web.struts
Controller for sequence export tile.
SequenceExportOptionsController() - Constructor for class org.intermine.bio.web.struts.SequenceExportOptionsController
 
SequenceFeatureDisplayer - Class in org.intermine.bio.web.displayer
Displayer for gene sequence feature
SequenceFeatureDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.SequenceFeatureDisplayer
Construct with config and the InterMineAPI.
SequenceFeatureExportOptionsController - Class in org.intermine.bio.web.struts
Controller for sequence, gff3 and bed format tiles.
SequenceFeatureExportOptionsController() - Constructor for class org.intermine.bio.web.struts.SequenceFeatureExportOptionsController
 
SequenceFeatureExportUtil - Class in org.intermine.bio.web.logic
Utility methods for LocatedSequenceFeature exporting.
SequenceFeatureExportUtil.InvalidQueryException - Exception in org.intermine.bio.web.logic
 
SequenceHttpExporter - Class in org.intermine.bio.web.export
Obsoleted - replaced by new results table An implementation of TableExporter that exports sequence objects using the BioJava sequence and feature writers.
SequenceHttpExporter() - Constructor for class org.intermine.bio.web.export.SequenceHttpExporter
 
sequenceKeys - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
sequenceNumber - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
sequenceOffset - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
SequenceOntology - Class in org.intermine.bio.ontology
Helper class for SequenceOntology.
SequenceOntology(String, InputStream) - Constructor for class org.intermine.bio.ontology.SequenceOntology
Constructor.
SequenceOntologyFactory - Class in org.intermine.bio.ontology
Class in charge of making sequence ontology objects
SequenceProcessor - Class in org.intermine.bio.dataconversion
A processor for the chado sequence module.
SequenceProcessor(ChadoDBConverter) - Constructor for class org.intermine.bio.dataconversion.SequenceProcessor
Create a new SequenceProcessor
SequenceService - Class in org.intermine.webservice.server.clob
A service to provide access to substrings of ClobAccess data.
SequenceService(InterMineAPI) - Constructor for class org.intermine.webservice.server.clob.SequenceService
 
sequential - Variable in class org.intermine.objectstore.query.Results
 
SERIAL_NUMBER - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key used to store the serial number identifying the production db
SERIAL_SEQUENCE_NAME - Static variable in class org.intermine.task.BuildDbTask
 
serialize(Properties) - Static method in class org.intermine.util.PropertiesUtil
Serialize properties to a string suitable for a subsequent load()
serializedSortOrderToMap(String) - Static method in class org.intermine.metadata.StringUtil
Make a Map from the serialized String returned by jQuery.sortable("serialize").
serveToken(DeletionToken) - Method in class org.intermine.webservice.server.user.NewDeletionTokenService
Serve a token to the outside world.
Service - Class in org.intermine.webservice.client.core
This class provides the base level common functionality required to access any InterMine service.
Service(String, String, String) - Constructor for class org.intermine.webservice.client.core.Service
Constructor.
service(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.WebService
Starting method of web service.
SERVICE_FAILED_MSG - Static variable in class org.intermine.webservice.server.WebServiceConstants
Error message returned in case of unexpected service failure.
serviced - Static variable in class org.intermine.objectstore.query.PrefetchManager
Set of requests currently being serviced.
ServiceException - Exception in org.intermine.webservice.client.exceptions
ServiceException is a base class for all service exceptions.
ServiceException(String) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceException
 
ServiceException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceException
 
ServiceException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceException
 
ServiceException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceException
Exception is filled in with some detailed information from response.
ServiceException - Exception in org.intermine.webservice.server.exceptions
ServiceException is a base class for all service exceptions.
ServiceException(String) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
 
ServiceException(String, int) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
 
ServiceException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
 
ServiceException(String, Throwable, int) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
 
ServiceException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
 
ServiceException(Throwable, int) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
 
ServiceFactory - Class in org.intermine.webservice.client.core
The Class that should be used for creating services.
ServiceFactory(String) - Constructor for class org.intermine.webservice.client.core.ServiceFactory
Construct a service factory with a default application name.
ServiceFactory(String, String) - Constructor for class org.intermine.webservice.client.core.ServiceFactory
Construct a factory for gaining access to specific resources.
ServiceFactory(String, String, String) - Constructor for class org.intermine.webservice.client.core.ServiceFactory
Deprecated.
This method causes username and password information to be insecurely transmitted over HTTP connections. Use the token authentication mechanism instead.
ServiceForbiddenException - Exception in org.intermine.webservice.client.exceptions
The ServiceForbiddenException is thrown by a service when an attempt is made to service that is disabled.
ServiceForbiddenException(String) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceForbiddenException
 
ServiceForbiddenException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceForbiddenException
 
ServiceForbiddenException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceForbiddenException
 
ServiceForbiddenException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceForbiddenException
 
ServiceForbiddenException - Exception in org.intermine.webservice.server.exceptions
The ServiceForbiddenException is thrown by a service when an attempt is made to service that is disabled.
ServiceForbiddenException(String) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceForbiddenException
 
ServiceForbiddenException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceForbiddenException
 
ServiceForbiddenException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceForbiddenException
 
ServiceListingHandler - Class in org.intermine.webservice.server
 
ServiceListingHandler() - Constructor for class org.intermine.webservice.server.ServiceListingHandler
 
ServicesListingsServlet - Class in org.intermine.webservice.server
Provide a list of all the services available at this mine.
ServicesListingsServlet() - Constructor for class org.intermine.webservice.server.ServicesListingsServlet
 
serviceThreads - Static variable in class org.intermine.objectstore.query.PrefetchManager
 
ServiceUnavailableException - Exception in org.intermine.webservice.client.exceptions
The ServiceUnavailableException is thrown when an exception occurs that is temporary, the user should try it again.
ServiceUnavailableException(String) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceUnavailableException
 
ServiceUnavailableException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceUnavailableException
 
ServiceUnavailableException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceUnavailableException
 
ServiceUnavailableException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceUnavailableException
 
SessionActivationListener - Class in org.intermine.web.logic.session
Added to each session to monitor activation events.
SessionActivationListener() - Constructor for class org.intermine.web.logic.session.SessionActivationListener
 
sessionCreated(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionListener
sessionDestroyed(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionListener
sessionDidActivate(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionActivationListener
Called after a session is unserialised.
sessionIdentifier - Variable in class org.intermine.api.tracker.track.TrackAbstract
 
SessionlessRequest - Class in org.intermine.webservice.server.core
 
SessionlessRequest(HttpServletRequest) - Constructor for class org.intermine.webservice.server.core.SessionlessRequest
Construct a request by wrapping the given request.
SessionListener - Class in org.intermine.web.logic.session
Perform InterMine-specific actions when a Session is constructed or destroyed
SessionListener() - Constructor for class org.intermine.web.logic.session.SessionListener
 
SessionMethods - Class in org.intermine.web.logic.session
Business logic that interacts with session data.
SessionService - Class in org.intermine.webservice.server
Open a new 24-hour session.
SessionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.SessionService
 
sessionWillPassivate(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionActivationListener
Called just before serialising to disk.
set(int, boolean) - Method in class org.intermine.util.IntPresentSet
Adds the given int to the set.
set(int, Object) - Method in class org.intermine.webservice.client.results.ResultRowList
 
setAccepted(Boolean) - Method in class org.intermine.api.bag.SharingInvite
 
setAccessions(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setAction(String) - Method in class org.intermine.task.Integrate
Set the action (retrieve or load) for this task.
setAction(String) - Method in class org.intermine.task.PostProcessTask
Set the action to perform - ie. the post-process
setAction(String) - Method in class org.intermine.web.struts.WidgetForm
 
setActionType(String) - Method in class org.intermine.web.struts.TemplateSettingsForm
 
setAdditionsFile(File) - Method in class org.intermine.task.ModelMergerTask
The file containing model additions.
setAdditionsFiles(List<File>) - Method in class org.intermine.task.ModelMergerTask
The files containing model additions.
setAlias(String) - Method in class org.intermine.sql.query.AbstractTable
Sets the alias for this AbstractTable object.
setAlias(String) - Method in class org.intermine.task.CreateIndexesTask
Set the ObjectStore alias.
setAlias(String) - Method in class org.intermine.task.DropPrecomputedTablesTask
Set the ObjectStore alias
setAlias(String) - Method in class org.intermine.task.PrecomputeTask
Set the ObjectStore alias.
setAlias(String) - Method in class org.intermine.task.RunIqlQueryTask
Set the ObjectStore alias.
setAlias(String) - Method in class org.intermine.task.SummariseObjectStoreTask
Set the ObjectStore alias
setAlias(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Set the ObjectStore alias
setAllFieldDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Sets up the object a little.
setAllowduplicates(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter
Toggle whether or not to allow duplicate sequences
setAllSelectedColumn(int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Select a whole column.
setAllSources(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
Set the list of data sources present in the project.xml, for the purposes of verifying the priorities properties file.
setAPI(InterMineAPI) - Method in class org.intermine.api.template.ApiTemplate
Only used on export so we can get the tags related to this template.
setApiKey(String) - Method in class org.intermine.api.profile.Profile
Set the API token for this user, and save it in the backing DB.
setAppendConfig(Boolean) - Method in class org.intermine.web.logic.config.HeaderConfigTitle
Set whether to append config from parent
setApplicationName(String) - Method in class org.intermine.webservice.client.core.ServiceFactory
Set the application name used to identify your requests to the server
setAspectDisplayers(Map<String, List<Displayer>>) - Method in class org.intermine.web.logic.config.Type
 
setAspects(String) - Method in class org.intermine.web.logic.config.Displayer
Set the aspects of this displayer
setAspects(ServletContext, Map<String, Aspect>) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the Map of aspects.
setAttribute(Integer, String, String) - Method in class org.intermine.bio.dataconversion.ChadoProcessor
Set an attribute in an Item by creating an Attribute object and storing it.
setAttribute(String, Object) - Static method in class org.intermine.web.context.InterMineContext
Set an attribute of the context.
setAttribute(String, String) - Method in class org.intermine.xml.full.Item
Add an attribute to this item.
setAttributeIndexes(boolean) - Method in class org.intermine.task.CreateIndexesTask
Set the attributeIndexes flag.
setAttributeOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of attributeOp
setAttributeOps(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm
Set the attribute ops
setAttributeOps(String, String) - Method in class org.intermine.web.struts.TemplateForm
Set an attribute op
setAttributeOptions(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of attributeOptions
setAttributeToEmptyString(String) - Method in class org.intermine.xml.full.Item
Add an attribute to this item and set it to the empty string.
setAttributeValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of attributeValue
setAttributeValues(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm
Set the attribute values
setAttributeValues(String, Object) - Method in class org.intermine.web.struts.TemplateForm
Set an attribute value
setAuthentication(String, String) - Method in class org.intermine.webservice.client.core.Service
Deprecated.
Use token based authentication instead (Service.setAuthentication(String) as this method will cause your user name and password to be transmitted insecurely across HTTP connections.
setAuthentication(String) - Method in class org.intermine.webservice.client.core.Service
Set the token to be used for authentication.
setAuthToken(String) - Method in interface org.intermine.webservice.client.core.Request
Set the authentication token for the request
setAuthToken(String) - Method in class org.intermine.webservice.client.core.RequestImpl
 
setAutoCompleter(ServletContext, AutoCompleter) - Static method in class org.intermine.web.logic.session.SessionMethods
Set the AutoCompleter into the ServletContext.
setBag(InterMineBag) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setBag(String, Object) - Method in class org.intermine.web.struts.TemplateForm
Set the bag name.
setBagName(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
name of bag that this widget is using.
setBagName(String) - Method in class org.intermine.web.struts.FindInListForm
 
setBagName(String) - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Set the value of bagName
setBagName(String) - Method in class org.intermine.web.struts.WidgetForm
name of bag that this widget is using.
setBagOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of bagOp
setBagOp(String, String) - Method in class org.intermine.web.struts.TemplateForm
Set bag operation.
setBagSelected(boolean) - Method in class org.intermine.web.logic.query.DisplayConstraint
Set if the bag is selected, used by the method isBagSelected that returns true, even if the constraint is an attribute constraint
setBagTableNames(Map<Object, String>) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
setBagType(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setBagType(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm
Set the bag type
setBagType(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setBagType(String) - Method in class org.intermine.web.struts.WidgetForm
 
setBagValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of bagValue
setBasedir(String) - Method in class org.intermine.task.Dependencies
Base directory that all projects are assumed relative to.
setBasedir(String) - Method in class org.intermine.task.MergeSourceModelsTask
Base directory that all projects are assumed relative to.
setBaseLink(String) - Method in class org.intermine.web.tags.table.NavigationBarTag
 
setBatchSize(int) - Method in class org.intermine.api.query.PathQueryExecutor
Sets batch size.
setBatchSize(int) - Method in interface org.intermine.objectstore.proxy.LazyCollection
Sets the number of rows requested from the ObjectStore whenever an execute call is made
setBatchSize(int) - Method in class org.intermine.objectstore.proxy.ProxyCollection
Sets the number of rows requested from the ObjectStore whenever an execute call is made
setBatchSize(int) - Method in class org.intermine.objectstore.query.Results
Sets the number of rows requested from the ObjectStore whenever an execute call is made
setBatchSize(int) - Method in class org.intermine.objectstore.query.ResultsBatches
Sets the number of rows requested from the ObjectStore whenever an execute call is made
setBatchWriter(BatchWriter) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Allows the changing of the BatchWriter that this ObjectStoreWriter uses.
setBatchWriter(BatchWriter) - Method in class org.intermine.sql.writebatch.Batch
Changes the BatchWriter for a new one.
setBiogridOrganisms(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter
Sets the list of taxonIds that should be imported if using split input files.
setBlockCount(int) - Method in class org.intermine.bio.io.bed.BEDRecord
 
setBlockCount(int) - Method in class org.intermine.bio.io.gaf.GAFRecord
 
setBlockSizes(List<Integer>) - Method in class org.intermine.bio.io.bed.BEDRecord
 
setBlockSizes(List<Integer>) - Method in class org.intermine.bio.io.gaf.GAFRecord
 
setBlockStarts(List<Integer>) - Method in class org.intermine.bio.io.bed.BEDRecord
 
setBlockStarts(List<Integer>) - Method in class org.intermine.bio.io.gaf.GAFRecord
 
setBoring(String) - Method in class org.intermine.task.InheritanceDotTask
Set a list of classnames that are boring - all classes that only extend one of these will be omitted from the graph.
setBuildDependencies(boolean) - Method in class org.intermine.task.Dependencies
Set whether or not to build project dependencies (default is true).
setBuildDir(String) - Method in class org.intermine.web.task.IssueTokenTask
Bean-style setter, as per the ant spec.
setCacheDirName(String) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
Set the cache file name
setCaseSensitive(boolean) - Method in class org.intermine.web.struts.BuildBagForm
 
setCategories(ServletContext, Set<String>) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the aspect categories into the servlet context.
setCategoryPath(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
SetCharacterEncodingFilter - Class in org.intermine.web.filters
Example filter that sets the character encoding to be used in parsing the incoming request, either unconditionally or only if the client did not specify a character encoding.
SetCharacterEncodingFilter() - Constructor for class org.intermine.web.filters.SetCharacterEncodingFilter
 
setCharSet(String) - Method in class org.intermine.webservice.client.core.ContentType
Sets character set of this content type.
setChildTermId(String) - Method in class org.intermine.bio.ontology.OboRelation
 
setChr(String) - Method in class org.intermine.bio.web.model.GenomicRegion
 
setChrLength(Integer) - Method in class org.intermine.bio.web.model.ChromosomeInfo
 
setChrom(String) - Method in class org.intermine.bio.io.bed.BEDRecord
 
setChrom(String) - Method in class org.intermine.bio.io.gaf.GAFRecord
 
setChromEnd(int) - Method in class org.intermine.bio.io.bed.BEDRecord
 
setChromEnd(int) - Method in class org.intermine.bio.io.gaf.GAFRecord
 
setChromosomeLocationsAndLengths() - Method in class org.intermine.bio.postprocess.CalculateLocations
For each SequenceFeature, if it has a Location on a Chromosome, set the SequenceFeature.chromosomeLocation reference to be that Location and set the length field of the SequenceFeature to chromosomeLocation.end - chromosomeLocation.start + 1
setChromStart(int) - Method in class org.intermine.bio.io.bed.BEDRecord
 
setChromStart(int) - Method in class org.intermine.bio.io.gaf.GAFRecord
 
setChrPID(String) - Method in class org.intermine.bio.web.model.ChromosomeInfo
 
setClassAttribute(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
The attribute of the class created to set with the identifying field.
setClassConfig(Type) - Method in class org.intermine.web.logic.config.FieldConfig
 
setClassDescriptor(ClassDescriptor) - Method in class org.intermine.metadata.FieldDescriptor
Set the parent ClassDescriptor - should be called when this is added to a ClassDescriptor.
setClassDescriptor(String) - Method in class org.intermine.xml.full.Item
Set the classDescriptor attribute to be the ClassDescriptor for the given className in the Model set by setModel().
setClasses(Map<String, Map<String, Object>>) - Method in class org.intermine.metadata.Model.ModelAST
 
setClassKeys(Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.bag.operations.BagOperation
 
setClassKeys(Map<String, List<FieldDescriptor>>) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
setClassLoader(ClassLoader) - Method in class org.intermine.web.task.CreateSearchIndexTask
Set the class loader
setClassName(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
The class name to use for objects created during load.
setClassName(String) - Method in class org.intermine.task.AnalyseDbTask
Set an optional class name, must also set model name
setClassName(String) - Method in class org.intermine.task.StaticMethodTask
Set class name on which to call static method.
setClassName(String) - Method in class org.intermine.web.logic.config.TableExportConfig
Set the className of this TableExportConfig
setClassName(String) - Method in class org.intermine.web.logic.config.Type
Set the unqualified class name for this Type (from fully-qualified)
setClassName(String) - Method in class org.intermine.web.logic.results.InlineResultsTableRow
 
setClassName(String) - Method in class org.intermine.web.struts.QueryClassSelectForm
Set the class name
setClassName(String) - Method in class org.intermine.xml.full.Item
Set the class of this item.
setClassNameOnTableRow(String, Object) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable
Set a class name on table row
setClassNameOnTableRow(String, Object) - Method in class org.intermine.web.logic.results.InlineResultsTable
Set a class name on table row, used for type safety as overriden on BagUploadConfirm
setClasspath(Path) - Method in class org.intermine.task.ReadResourceTask
The classpath to use when looking up a resource.
setClassPathRef(Reference) - Method in class org.intermine.task.MergeSourceModelsTask
Set the classpath to use for post processing.
setClassPathRef(Reference) - Method in class org.intermine.task.PostProcessTask
Set the classpath to use for post processing.
setClasspathRef(Reference) - Method in class org.intermine.task.ReadResourceTask
Set the classpath to use when looking up a resourca, given as reference to a Path defined elsewhere
setClsName(String) - Method in class org.intermine.task.DBConverterTask
Set the source specific subclass of FileConverter to run
setClsName(String) - Method in class org.intermine.task.DirectoryConverterTask
Set the source specific subclass of DirectoryConverter to run
setClsName(String) - Method in class org.intermine.task.FileConverterTask
Set the source specific subclass of FileConverter to run
setClsName(String) - Method in class org.intermine.task.PostProcessorTask
Set the name of the PostProcessor sub-class to load to do the postprocessing.
setCode(String) - Method in class org.intermine.web.logic.query.DisplayConstraint
 
setCode(String) - Method in class org.intermine.web.logic.template.ConstraintInput
 
setCollection(String, List<String>) - Method in class org.intermine.xml.full.Item
Set a collection.
setColumnId(String) - Method in class org.intermine.api.results.Column
 
setColumnNames(List<String>) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Set the column names
setColumnNames(List<String>) - Method in class org.intermine.web.tags.table.TableTag
 
setColumnTitle(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
setComment(String) - Method in class org.intermine.template.TemplateQuery
Set the private comment for this template.
setComment(String) - Method in class org.intermine.web.struts.TemplateSettingsForm
Set the comment
setCommentEvidence(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setComments(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setCommentType(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
Creates a new temporary object to hold the type and later the publications for this comment.
setComplete(long) - Method in class org.intermine.objectstore.query.ResultsInfo
Sets the estimated amount of time taken to produce the entire set of results.
setComplexesSource(String) - Method in class org.intermine.bio.dataconversion.PsiComplexesConverter
Sets the database, e.g.
setComputeTotalCount(boolean) - Method in class org.intermine.webservice.server.query.result.QueryResultInput
Sets true if compute total count of all available results.
setConfigFile(File) - Method in class org.intermine.task.AcceptanceTestTask
Set the File to read configuration from
setConfigFileName(String) - Method in class org.intermine.task.SummariseObjectStoreTask
Set the name of the Properties file containing the names of the classes and fields to summarise.
setConfigurationFile(File) - Method in class org.intermine.task.TSVFileReaderTask
Set the configuration file to use.
setConnectField(String) - Method in class org.intermine.api.bag.BagQueryConfig
Set the connecting field for adding an extra constraint to bag queries.
setConnectionTimeout(int) - Method in class org.intermine.webservice.client.core.Service
Sets connection timeout.
setConstrainField(String) - Method in class org.intermine.api.bag.BagQueryConfig
Set the field to constrain when making an extra constraint.
setConstraint(TemplateQuery, TemplateValue) - Static method in class org.intermine.api.template.TemplatePopulator
Set the value for a constraint in the template query with the given TemplateValue.
setConstraint(Constraint) - Method in class org.intermine.objectstore.query.Query
Constrain this Query using either a single constraint or a set of constraints
setConstraint(Constraint) - Method in interface org.intermine.objectstore.query.Queryable
Sets the additional constraint.
setConstraint(Constraint) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Sets the additional constraint.
setConstraint(Constraint) - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Sets the additional constraint.
setConstraintDescription(PathConstraint, String) - Method in class org.intermine.template.TemplateQuery
Sets the description for a constraint.
setConstraintLogic(String) - Static method in class org.intermine.dwr.AjaxServices
Set the constraint logic on a query to be the given expression.
setConstraintLogic(String) - Method in class org.intermine.pathquery.PathQuery
Sets the current constraint logic.
setConstraintOp(ConstraintOp) - Method in class org.intermine.web.logic.template.ConstraintInput
Sets constraint operation.
setConstraints(Map<String, List<ConstraintInput>>) - Method in class org.intermine.web.logic.template.TemplateResultInput
Sets constraints.
setConstraints(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setConstraintsForView(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
setContent(String) - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig
Set the content of the widget.
setContent(File) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo
Set the content for this creation request as coming from a file on the file-system.
setContent(InputStream) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo
Set the content for this creation request as coming from an InputStream.
setContent(Collection<String>) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo
Set the content for this request as coming from a set of strings, with each string representing one identifier.
setContent(String...) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo
Set the content for this request as coming from a set of strings, with each string representing one identifier.
setContent(String) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo
Set the content as coming from a string.
setContent(PathQuery) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo
Set the content for this request as a query to run to find objects with.
setContentType(ContentType) - Method in interface org.intermine.webservice.client.core.Request
 
setContentType(ContentType) - Method in class org.intermine.webservice.client.core.RequestImpl
setConverter(GFF3Converter) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
 
setConverter(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
Set the converter
setCorrection(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
 
setCorrectionCoefficient(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
setCount(int) - Method in class org.intermine.web.logic.session.QueryCountQueryMonitor
Set the query count/size.
setCountFormat() - Method in class org.intermine.webservice.client.core.RequestImpl
Set the format as count format.
setCreategenes(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter
Toggle whether or not to create genes and protein/gene associations.
setCreatego(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter
Toggle whether or not to import GO data
setCreateinterpro(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter
Deprecated.
The UniProt data source does not create interpro domains any longer. Please use the InterPro data source instead.
setCreaterelations(String) - Method in class org.intermine.bio.dataconversion.OboConverter
Set to false to prevent storing OntologyRelation objects that include the relationship types between terms.
setCSVContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets comma separated values content type.
setCSVHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets response header and content type for comma separated values output.
setCurrentFile(File) - Method in class org.intermine.dataconversion.FileConverter
Set the current File that is being processed.
setCurrentMapFromCurrentArray(ResultElement) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Finds the object we should be dealing with by getting it from the current array.
setCurrentMapFromCurrentArray() - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Sets the current map to work with by getting the last one from the current array.
setCurrentPage(Integer) - Method in class org.intermine.web.tags.table.NavigationBarTag
 
setCustomContentType(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets content type to the parameter specified
setCustomTypeHeader(HttpServletResponse, String, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets response header and content type for a custom content type.
setDatabase(String) - Method in class org.intermine.task.AcceptanceTestTask
Set the database alias
setDatabase(String) - Method in class org.intermine.task.GrantTask
Set the database alias
setDataDir(String) - Method in class org.intermine.task.DirectoryConverterTask
Set the dataDir.
setDataSet(String) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter
Update the dataset reference Id.
setDataSet(String) - Method in class org.intermine.bio.dataconversion.BioStoreHook
Update the dataset reference Id.
setDatasetRefId(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setDataSets(Model, Item, String, String) - Static method in class org.intermine.bio.dataconversion.BioStoreHook
Do the work of processItem() by setting DataSet and DataSource references and collections on the given Item.
setDataSetTitle(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
If a value is specified this title will used when a DataSet is created.
setDataSetTitle(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
Set the dataSetTitle
setDataSourceName(String) - Method in class org.intermine.bio.dataconversion.BioDBConverter
Set the name of the DataSource Item to create for this converter.
setDataSourceName(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
Datasource for any bioentities created
setDataSourceName(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
Set the dataSourceName
setDate(Date) - Method in class org.intermine.api.profile.InterMineBag
Sets date when bag was created.
setDb(Database) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
setDbAlias(String) - Method in class org.intermine.task.DBConverterTask
Set the Database to read from
setDbrefs(Map<String, Set<String>>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setDefaultValue(String, String) - Method in class org.intermine.webservice.server.widget.WidgetsRequestParser
Set a parameter default.
setDeleteTracks(boolean) - Method in class org.intermine.web.struts.TemplatesImportForm
Set the deleteTracks flag.
SetDeployURL - Class in org.intermine.task
 
SetDeployURL() - Constructor for class org.intermine.task.SetDeployURL
 
setDescr(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setDescription(String) - Method in class org.intermine.api.profile.InterMineBag
 
setDescription(String) - Method in class org.intermine.api.template.ApiTemplate
 
setDescription(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder
 
setDescription(String) - Method in class org.intermine.bio.ontology.OboTerm
Set the term description.
setDescription(String, String) - Method in class org.intermine.pathquery.PathQuery
Sets the description for a given path.
setDescription(String) - Method in class org.intermine.pathquery.PathQuery
Sets the description for this PathQuery.
setDescription(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setDescription(String) - Method in class org.intermine.web.struts.TemplateSettingsForm
Set the description
setDescriptor(FieldDescriptor) - Method in class org.intermine.web.logic.results.InlineList
Set FieldDescriptor so we can work with placements
setDestDir(File) - Method in class org.intermine.task.ModelOutputTask
Sets the directory that output should be written to.
setDestDir(File) - Method in class org.intermine.task.RetrieveMetadataTask
Sets the destination directory
setDestFile(File) - Method in class org.intermine.objectstore.intermine.TorqueModelOutputTask
Sets the file to which the data should be written.
setDirect(boolean) - Method in class org.intermine.bio.ontology.OboRelation
 
setDirectChildren(Set<ChadoCVTerm>) - Method in class org.intermine.bio.chado.ChadoCVTerm
Set the direct children of this term.
setDirectory(String) - Method in class org.intermine.task.InheritanceDotTask
Set the directory containing java source files, such as one might use in the sourceclasspath.
setDirectParents(Set<ChadoCVTerm>) - Method in class org.intermine.bio.chado.ChadoCVTerm
Set the direct parents of this term.
setDisableResultsCache(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Sets the disableResultsCache configuration option.
setDisableResultsCache(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Sets the disableResultsCache configuration option.
setDisease(String, String) - Method in class org.intermine.bio.dataconversion.UniprotConverter.DiseaseHolder
 
setDisplayer(String) - Method in class org.intermine.web.logic.config.FieldConfig
Set the displayer
setDisplayFields(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
setDistinct(boolean) - Method in class org.intermine.objectstore.query.Query
Set the value of the distinct property, which determines whether duplicates are permitted in the results returned by this Query
setDistinct(boolean) - Method in class org.intermine.sql.query.Query
Sets the distinct status of this query.
setDoGzip(boolean) - Method in class org.intermine.web.struts.TableExportForm
Set whether the output should be GZIPped.
setDomain(String) - Method in class org.intermine.api.beans.PartnerLink
 
setDomainLabel(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
Set the value of domainLabel
setDomains(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setDoNotTruncate(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
If set to true, don't truncate long fields or put in a [View all...] link in the object details page.
setDontCreateLocations(boolean) - Method in class org.intermine.bio.dataconversion.GFF3Converter
Set the dontCreateLocations flag
setDontCreateLocations(boolean) - Method in class org.intermine.bio.task.GFF3ConverterTask
Set the dontCreateLocations flag, the default is false - create locations.
setDuplicate(boolean) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setEditable(PathConstraint, boolean) - Method in class org.intermine.template.TemplateQuery
Sets a constraint to be editable or not.
seteditable(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setEditable(boolean) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Set the editable flag (when building a template).
setEditableConstraints(List<PathConstraint>) - Method in class org.intermine.template.TemplateQuery
Sets the list of editable constraints to exactly that provided, in the given order.
setEditableInTemplate(boolean) - Method in class org.intermine.web.logic.query.DisplayConstraint
 
setEdited(boolean) - Method in class org.intermine.template.TemplateQuery
Set the query as being edited.
setEditingConstraintCode(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Set the code of an existing constraint that is being edited.
setEmail(String) - Method in class org.intermine.web.task.IssueTokenTask
Bean-style setter, as per the ant spec.
setEmptyResultSet(boolean) - Method in class org.intermine.bio.dataconversion.EnsemblSnpDbConverter
For unit test perpose, when result set is empty, set to true
setEnd(int) - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
Set end value
setEnd(Integer) - Method in class org.intermine.bio.web.model.GenomicRegion
 
setEnrich(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
setEnrichIdentifier(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
setEnsemblcomparaHomologues(String) - Method in class org.intermine.bio.dataconversion.EnsemblComparaConverter
Sets the list of organisms to process only if the genes are homologues for organism of interest.
setEnsemblcomparaOrganisms(String) - Method in class org.intermine.bio.dataconversion.EnsemblComparaConverter
Process all homologues for this organism.
setEnsemblDb(String) - Method in class org.intermine.bio.postprocess.PostProcessOperationsTask
Sets the value of ensemblDb
setEnsemblPrefix(String) - Method in class org.intermine.bio.util.OrganismData
 
setEof(HintingFetcher) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Sets the equivalent object fetcher.
setErr(OutputStream) - Method in class org.intermine.web.task.KeyStoreTask
Set the error handler
setError(String, int) - Method in class org.intermine.webservice.server.output.Output
Sets the error message
setErrorCorrection(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setErrorCorrection(String) - Method in class org.intermine.web.struts.WidgetForm
 
setErrorOnInitialiser(ServletContext, Map<String, String>) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the blocking error codes into the servlet context.
setEscapeXml(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
If set to true, don't escape the field value on object details page.
setEstimatedRows(long) - Method in class org.intermine.sql.query.ExplainResult
Use this to provide the object with a "better" estimate of the number of rows in the results of this Query.
setExcludeList(String) - Method in class org.intermine.task.ConverterTask
Sets the list of classes to NOT try and convert
setExistingBagName(String) - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Sets the value of existingBagName
setExistingBagName(String) - Method in class org.intermine.web.struts.SaveBagForm
Sets the value of existingBagName
setExpiry(String) - Method in class org.intermine.web.task.IssueTokenTask
Bean-style setter, as per the ant spec.
setExplain(boolean) - Method in class org.intermine.sql.query.Query
Sets the explain status of this query.
setExportField(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
setExporttype(String) - Method in class org.intermine.web.struts.WidgetForm
 
setExpression(String) - Method in class org.intermine.task.XPathSelect
Set the XPath expression.
setExtededRegionSize(int) - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint
 
setExtendedEnd(Integer) - Method in class org.intermine.bio.web.model.GenomicRegion
 
setExtendedRegionSize(int) - Method in class org.intermine.bio.web.model.GenomicRegion
 
setExtendedStart(Integer) - Method in class org.intermine.bio.web.model.GenomicRegion
 
setExtension(int) - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
 
setExternalLink(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
setExternalLink(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
setExternalLink(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setExternalLinkLabel(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
setExtraAttribute(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
 
setExtraConstraintClassName(String) - Method in class org.intermine.api.bag.BagQueryConfig
Set the class name of extra constraint to use in BagQuery objects using this config object.
setExtraFieldValue(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm
Set the extra field value
setExtraFieldValue(String) - Method in class org.intermine.web.struts.BuildBagForm
Set the extra field value.
setExtraFieldValue(String) - Method in class org.intermine.web.struts.ModifyBagDetailsForm
 
setExtraModelPathsEnd(String) - Method in class org.intermine.task.MergeSourceModelsTask
The paths containing extra model additions that should be merged last.
setExtraModelPathsStart(String) - Method in class org.intermine.task.MergeSourceModelsTask
The paths containing extra model additions that should be merged first.
setExtraThreads(int) - Method in class org.intermine.task.CreateIndexesTask
Set the number of extra worker threads.
setExtraValue(String) - Method in class org.intermine.web.logic.template.ConstraintInput
Sets extra value
setExtraValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of extraValue
setExtraValue(String) - Method in class org.intermine.webservice.server.lists.ListsServiceInput
An extra value, such as an organism, for use in lookup constraints.
setExtraValues(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm
Sets the extra values
setExtraValues(String, Object) - Method in class org.intermine.web.struts.TemplateForm
Set an extra value
setFactory(ServiceFactory) - Method in class org.intermine.webservice.client.core.Service
Set the ServiceFactory this service can use to access other services.
setFastaTaxonId(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
Set the Taxon Id of the Organism we are loading.
setFavourite(String, String, boolean) - Method in class org.intermine.dwr.AjaxServices
Creates a favourite Tag for the given templateName
setFeature(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Set the feature item for this record.
setFeatureTypes(Set<Class<?>>) - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint
 
setFeatureTypes(Collection<String>) - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
Set the feature types for this request.
setFetchFields(boolean, Set<FieldDescriptor>) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Sets variables which determines which fields are prefetched.
setField(Object) - Method in class org.intermine.api.results.ResultElement
Set the field value
SetFieldConfigAction - Class in org.intermine.bio.chado.config
An action that sets an attribute in a new Item.
SetFieldConfigAction(String) - Constructor for class org.intermine.bio.chado.config.SetFieldConfigAction
Create a new SetFieldConfigAction that sets the given field.
SetFieldConfigAction(String, Pattern) - Constructor for class org.intermine.bio.chado.config.SetFieldConfigAction
Create a new SetFieldConfigAction that sets the given field.
setFieldExporter(String) - Method in class org.intermine.web.logic.config.FieldConfig
Set the class name of the FieldExporter to use when this field is viewed.
setFieldExpr(String) - Method in class org.intermine.web.logic.config.FieldConfig
Set the JSTL expression for this field which will be evaluated in the request context when the JSP is viewed.
setFieldToAlias(FromElement, Map<String, String>) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
setFieldValue(String, Object) - Method in interface org.intermine.model.FastPathObject
Sets the value of a field by name.
setFieldValue(String, Object) - Method in class org.intermine.objectstore.proxy.ProxyReference
Sets the value of a field by name.
setFieldValue(Object, String, Object) - Static method in class org.intermine.util.DynamicUtil
Sets the value of a public or protected Field of an Object given the field name.
setFile(String) - Method in class org.intermine.bio.task.OboConverterTask
Set the input file name
setFile(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask
Set a file name to load from
setFile(File) - Method in class org.intermine.task.FileName
 
setFile(String) - Method in class org.intermine.task.FullXmlConverterTask
Set a file name to load from
setFile(String) - Method in class org.intermine.task.InheritanceDotTask
Set the name of the new dot file.
setFile(File) - Method in class org.intermine.task.XPathSelect
Set the file to write to.
setFileArray(File[]) - Method in class org.intermine.bio.dataconversion.EnsembSnpLoaderTask
Directly set the array of files to read from.
setFileArray(File[]) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
Directly set the array of files to read from.
setFileArray(File[]) - Method in class org.intermine.bio.dataconversion.VcfLoaderTask
Directly set the array of files to read from.
setFileName(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets the content disposition filename.
setFileName(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
Set the name of the file to write to.
setFileName(String) - Method in class org.intermine.web.task.ProfileReadTask
Set the name of the file to read from.
setFileName(String) - Method in class org.intermine.web.task.ProfileWriteTask
Set the name of the file to write to.
setFileName(String) - Method in class org.intermine.web.task.TemplateTrackReadTask
Set the name of the file to read from.
setFileName(String) - Method in class org.intermine.web.task.TemplateTrackWriteTask
Set the name of the file to write to.
setFilter(String) - Method in class org.intermine.web.logic.widget.EnrichmentWidget
 
setFilter(String) - Method in class org.intermine.web.logic.widget.GraphWidget
 
setFilter(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setFilter(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
 
setFilterLabel(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setFilterLabel(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setFilters(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setFilters(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setFlattenedResults() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
builds, runs query.
setFormat(String) - Method in class org.intermine.web.struts.CSVExportForm
Set the format.
setFormat(String) - Method in class org.intermine.webservice.client.core.RequestImpl
Set the format for the request.
setFormat(Format) - Method in class org.intermine.webservice.server.WebService
For very picky services, you can just set it yourself, and say "s****w you requester".
setFormFile(FormFile) - Method in class org.intermine.web.struts.BuildBagForm
Set the FormFile.
setFormFile(FormFile) - Method in class org.intermine.web.struts.ImportXMLForm
Set the FormFile.
setFragment(boolean) - Method in class org.intermine.bio.dataconversion.UniprotEntry
dev can configure converter to load these or not.
setFull(boolean) - Method in class org.intermine.task.AnalyseDbTask
Set true if a VACUUM FULL ANALYSE required
setGaff(String) - Method in class org.intermine.bio.dataconversion.GoConverter
Sets the file format for the GAF. 2.0 is the default.
setGeneDesignation(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
set the gene designation for this taxon. can be NULL
setGeneFile(File) - Method in class org.intermine.bio.dataconversion.TreefamConverter
Set the gene input file.
setGeneratedClassesAvailable(boolean) - Method in class org.intermine.metadata.Model
Sets if generated classes are available.
setGeneSource(FeatureData, String) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
Method to set the source for gene for modencode datasources it will add the title
setGeneSource(Integer, String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
to set source field if in the model (modmine)
setGeneSource(FeatureData, String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
set the source field for modENCODE gene
setGenomeBuild(String) - Method in class org.intermine.bio.web.model.OrganismInfo
 
setGenomicRegionList(List<GenomicRegion>) - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint
 
setGlobalSearchRepository(ServletContext, SearchRepository) - Static method in class org.intermine.web.logic.session.SessionMethods
Set the SearchRepository for global (public) objects in the servlet context.
setGOTerms(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setGraphType(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setGzippedContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets gzip content type ("application/octet-stream")
setGzippedHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets response header and content type for gzipped output.
setHandlerClassName(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
Set the name of GFF3RecordHandler class to use when processing.
setHeader(String, String) - Method in interface org.intermine.webservice.client.core.Request
Sets a request header.
setHeader(String, String) - Method in class org.intermine.webservice.client.core.RequestImpl
Sets a request header.
setHeaderAttributes(Map<String, Object>) - Method in class org.intermine.webservice.server.output.Output
Sets header attributes that are displayed for example in xml header.
setHeaderAttributes(Map<String, Object>) - Method in class org.intermine.webservice.server.output.StreamedOutput
Sets header attributes that are displayed for example in xml header.
setHeaderAttributes(String) - Method in class org.intermine.webservice.server.query.QueryToListService
Sets the header attributes map on the current output object.
setHeaderAttributes(PathQuery, Integer, Integer) - Method in class org.intermine.webservice.server.query.result.QueryResultService
Set the header attributes of the output based on the values of the PathQuery
setHeaderAttributes(PathQuery, Integer, Integer) - Method in class org.intermine.webservice.server.query.result.TableRowService
 
setHide(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
If set to true, do not display field on report page.
setHighlight(String) - Method in class org.intermine.web.struts.WidgetForm
 
setHomologeneHomologues(String) - Method in class org.intermine.bio.dataconversion.HomologeneConverter
Sets the list of taxonIds of homologues that should be processed.
setHomologeneOrganisms(String) - Method in class org.intermine.bio.dataconversion.HomologeneConverter
Sets the list of taxonIds that should be processed.
setHTMLContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets HTML content type.
setIconImage(String) - Method in class org.intermine.web.logic.aspects.Aspect
Set the icon Image
setId(String) - Method in class org.intermine.bio.io.gff3.GFF3Record
Set the Id of this GFF3Record.
setId(String) - Method in class org.intermine.bio.ontology.OboTypeDefinition
 
setId(Integer) - Method in interface org.intermine.model.InterMineFastPathObject
Setter for the ID field.
setId(Integer) - Method in interface org.intermine.model.InterMineObject
Setter for the ID field.
setId(Integer) - Method in class org.intermine.objectstore.proxy.ProxyReference
Sets the ID value
setId(String) - Method in class org.intermine.web.logic.config.TableExportConfig
Set the id of this TableExportConfig
setId(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setId(String) - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Sets element id.
setIdentifier(String) - Method in class org.intermine.api.beans.ObjectDetails
 
setIdentifier(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter.DiseaseHolder
 
setIdentifier(String) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
Set identifier
setIdentifier(String) - Method in class org.intermine.xml.full.Item
Set the identifier of this item.
setIdentifierMap(Map<?, ?>) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Set the Map of GFF identifiers to Item identifier.
setIdentifierName(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
 
setIdSuffix(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
Set the suffix to add to identifiers from the FASTA file when creating BioEnitys.
setIdx(int) - Method in class org.intermine.bio.web.model.OrganismInfo
 
setIgnore(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Set a comma separated list of template names to ignore - i.e. not precompute.
setIgnoreDuplicates(boolean) - Method in interface org.intermine.dataloader.IntegrationWriter
Tell this IntegrationWriter whether to ignore duplicate objects from the same source.
setIgnoreDuplicates(boolean) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Tell this IntegrationWriter whether to ignore duplicate objects from the same source.
setIgnoreDuplicates(boolean) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
Set the value of ignoreDuplicates for the IntegrationWriter.
setIgnoreDuplicates(boolean) - Method in class org.intermine.dataloader.XmlDataLoaderTask
Set the value of ignoreDuplicates for the IntegrationWriter
setIgnoreDuplicates(boolean) - Method in class org.intermine.task.DirectDataLoaderTask
Set the value of ignoreDuplicates for the IntegrationWriter
setImage(String) - Method in class org.intermine.web.logic.config.HeaderConfigLink
Set
setImageName(String) - Method in class org.intermine.bio.web.XRef
 
setImmutable() - Method in class org.intermine.objectstore.query.Results
Tells this Results object that it is being put into a cache, so it needs to be made immutable to prevent threads stomping on each other and changing settings.
setImplementations(String) - Method in class org.intermine.xml.full.Item
Set the "implements" of this item.
setIncludeHeaders(boolean) - Method in class org.intermine.web.struts.TableExportForm
Set the includeHeaders flag.
setIndex(int) - Method in class org.intermine.api.results.Column
Sets the value of index
setInputModelFile(File) - Method in class org.intermine.task.ModelMergerTask
Set the model to add additions to.
setIntactOrganisms(String) - Method in class org.intermine.bio.dataconversion.PsiConverter
Sets the list of taxonIds that should be imported if using split input files.
setIntegrationWriter(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
Set the IntegrationWriter.
setIntegrationWriter(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask
Set the IntegrationWriter.
setIntegrationWriterAlias(String) - Method in class org.intermine.task.DirectDataLoaderTask
Set the IntegrationWriter.
setInterbase(boolean) - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
 
setInterMineAPI(ServletContext, InterMineAPI) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the InterMineAPI in the servlet context.
setIntroText(String) - Method in class org.intermine.web.logic.aspects.Aspect
Set the introduction text
setInvite(String) - Method in class org.intermine.web.struts.InvitationForm
 
setIsoform(boolean) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setItemRgb(int) - Method in class org.intermine.bio.io.bed.BEDRecord
 
setItemRgb(int) - Method in class org.intermine.bio.io.gaf.GAFRecord
 
setJavaClass(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Set the Java class name of the controller for this displayer.
setJoinType(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
setJSONContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets the content type to "application/json"
setJSONFormat() - Method in class org.intermine.webservice.client.core.RequestImpl
Set the format as JSON-Object format.
setJSONHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets the response header and content type for json output
setJSONHeader(HttpServletResponse, String, boolean) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets the response header and content type for json output
setJSONPContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets the content type to "text/javascript"
setJSONPHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets the response header and content type for jsonp output
setJSONRowsFormat() - Method in class org.intermine.webservice.client.core.RequestImpl
Set the format as JSON-Rows format.
setJSONSchemaContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets the content type to "application/schema+json"
setJSONSchemaHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Set the header for a JSON-schema response.
setJspName(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Set the name of the JSP associated with this displayer.
setKeggOrganisms(String) - Method in class org.intermine.bio.dataconversion.KeggOrthologuesConverter
Sets the list of taxonIds that should be imported
setKeggOrganisms(String) - Method in class org.intermine.bio.dataconversion.KeggPathwayConverter
Sets the list of taxonIds that should be imported
setKeyFieldNames(List<String>) - Method in class org.intermine.api.profile.InterMineBag
Set the keyFieldNames
setKeystoreFile(String) - Method in class org.intermine.web.task.KeyStoreTask
Bean-style setter for keystoreFile, as per ant spec.
setKeyToRetreive(String) - Method in class org.intermine.task.RetrieveMetadataTask
Set a key to retrieve from database.
setKeywords(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setLabel(String) - Method in class org.intermine.web.logic.config.FieldConfig
Set the label for this field-configuration.
setLabel(String) - Method in class org.intermine.web.logic.config.Type
Set the label property.
setLabel(String) - Method in class org.intermine.web.logic.query.DisplayConstraint
Set the label of the constraint.
setLabel(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
setLabel(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setLargeImage(String) - Method in class org.intermine.web.logic.aspects.Aspect
Set the webapp relative path to the large image.
setLayout(String) - Method in class org.intermine.web.logic.template.TemplateResultInput
 
setLayout(String) - Method in class org.intermine.webservice.server.query.result.QueryResultInput
 
setLdr(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setLength(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setLimit(int) - Method in class org.intermine.objectstore.query.Query
Sets the LIMIT parameter for this query - note that this is only honoured in a subquery.
setLimit(Integer) - Method in class org.intermine.webservice.server.WebServiceInput
Sets maximum of returned results.
setLimitOffset(int, int) - Method in class org.intermine.sql.query.Query
Sets the LIMIT and OFFSET numbers for this query.
setLineLength(Integer) - Method in class org.intermine.web.logic.config.InlineListConfig
Sets the amount of entries to show based on their total length
setLink(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setLink(String) - Method in class org.intermine.web.struts.WidgetForm
 
setLinkFile(File) - Method in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask
Set the linkFile attribute.
setLinkRedirect(String) - Method in class org.intermine.api.results.ResultElement
 
setListLeft(String) - Method in class org.intermine.web.struts.ModifyBagForm
 
setListPath(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setListRight(String) - Method in class org.intermine.web.struts.ModifyBagForm
 
setListsButton(String) - Method in class org.intermine.web.struts.ModifyBagForm
 
setListSize(Integer) - Method in class org.intermine.webservice.server.lists.ListUploadService
Sets the size of the list on the header attributes.
setLoadfragments(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter
Toggle whether or not to load fragments.
setLoadFullRecord(String) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
Load summary version of Publication record by default.
setLoadtrembl(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter
Toggle whether or not to load trembl data for all given organisms
setLocation(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Set the location item for this record.
setLocation(File) - Method in class org.intermine.task.project.Source
Set the location of this Source directory.
setLocation(String) - Method in class org.intermine.task.project.UserProperty
Set the property location
setLog(Writer) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Allows the log to be set in this objectstore.
setLog(Writer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Not implemented.
setLogBeforeExecute(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Sets the logBeforeExecute configuration option.
setLogBeforeExecute(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Sets the logBeforeExecute configuration option.
setLogEverything(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Sets the logEverything configuration option.
setLogEverything(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Sets the logEverything configuration option.
setLogExplains(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Sets the logExplains configuration option.
setLogExplains(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Sets the logExplains configuration option.
setLogTableName(String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Allows the log table name to be set in this objectstore.
setLogTableName(String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Not implemented.
setLoopQueryOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of loopQueryOp
setLoopQueryValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of loopQueryValue
setMailinglist(boolean) - Method in class org.intermine.web.struts.CreateAccountForm
 
setMainTitles(String) - Method in class org.intermine.web.logic.config.HeaderConfigTitle
Set main title(s) path(s) for the object, e.g.: symbol, primaryIdentifier => eve FBgn0000606
setMakeUcscCompatible(boolean) - Method in class org.intermine.bio.web.struts.BEDExportForm
Set whether to make exported BED compatible with UCSC genome browser.
setMakeUcscCompatible(boolean) - Method in class org.intermine.bio.web.struts.GFF3ExportForm
Set whether to make exported GFF3 compatible with UCSC genome browser.
setMatchIDs(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm
Set the encoded match ids.
setMatchOnFirst(boolean) - Method in class org.intermine.api.bag.BagQueryConfig
If flag is true, bagqueryrunner queries for identifier until match is found, returning only that first matching record.
setMaterialisedCollection(Collection<E>) - Method in class org.intermine.objectstore.proxy.ProxyCollection
Sets the collection with a new materialised collection.
setMax(int) - Method in class org.intermine.objectstore.query.ResultsInfo
Sets the maximum possible number of rows in the results.
setMax(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setMax(String) - Method in class org.intermine.web.struts.WidgetForm
 
setMaxCount(int) - Method in class org.intermine.webservice.client.core.RequestImpl
Sets the maximum number of rows returned.
setMaxP(double) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
 
setMaxQueryParseTime(long) - Method in class org.intermine.sql.precompute.QueryOptimiserContext
Set the maximum time in milliseconds that the optimiser should spend parsing a query from SQL string to an org.intermine.sql.Query object.
setMessage(String) - Method in class org.intermine.web.struts.ContactForm
 
setMethod(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder
terms describe the method used int he experiment, eg two hybrid, etc
setMethod(String) - Method in class org.intermine.task.StaticMethodTask
Name of method to call.
setMin(int) - Method in class org.intermine.objectstore.query.ResultsInfo
Sets the minimum possible number of rows in the results.
setMinBagTableSize(int) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Set the cutoff value used to decide if a bag should be put in a table.
setMinBagTableSize(int) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Set the cutoff value used to decide if a bag should be put in a table.
setMineId(Integer) - Method in class org.intermine.webservice.server.lists.ListsServiceInput
Sets Intermine unique object id
setMinRows(int) - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer
Set the minimum row count for precomputed queries.
setMinRows(Integer) - Method in class org.intermine.task.PrecomputeTask
Set the minimum row count for precomputed queries.
setMinRows(Integer) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Set the minimum row count for precomputed queries.
setMissingChromosomeLocations() - Method in class org.intermine.bio.postprocess.CalculateLocations
For each SequenceFeature, if it has a Location on a Chromosome, set the SequenceFeature.chromosomeLocation reference *if* the reference is not already set.
setMode(String) - Method in class org.intermine.sql.precompute.QueryOptimiserContext
Sets the optimiser mode of operation.
setModel(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
Set the name of model to create data in
setModel(Model) - Method in class org.intermine.metadata.ClassDescriptor
Set the model for this ClassDescriptor, this is only be called once and will throw an Exception if called again.
setModel(Model) - Method in class org.intermine.pathquery.Node
Attach the model.
setModel(String) - Method in class org.intermine.task.AnalyseDbTask
Set model name, must be set if class name specified
setModel(String) - Method in class org.intermine.task.BuildDbTask
Sets the model
setModel(String) - Method in class org.intermine.task.ModelOutputTask
Set the model to be used.
setModel(Model) - Method in class org.intermine.web.logic.query.MetadataNode
 
setModel(Model) - Method in class org.intermine.xml.full.Item
Set the Model to use when checking calls to the other set methods
setModelFile(File) - Method in class org.intermine.task.MergeSourceModelsTask
Set the model to add additions to.
setModelName(String) - Method in class org.intermine.task.ConverterTask
Set the target model name
setModelName(String) - Method in class org.intermine.task.StoreMetadataTask
Sets the model name
setMolecularWeight(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setMonkey(String) - Method in class org.intermine.web.struts.ContactForm
 
setMultiValueAttribute(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of multiValueAttribute, a string representing the values selected by the user separated by a comma.
setMultiValueAttribute(Map<String, String>) - Method in class org.intermine.web.struts.TemplateForm
Set the multivalueattribute
setMultiValueAttribute(String, String) - Method in class org.intermine.web.struts.TemplateForm
Set the multivalueattribute
setMultivalues(List<String>) - Method in class org.intermine.web.logic.template.ConstraintInput
Set multivalues
setMultiValues(Map<String, String[]>) - Method in class org.intermine.web.struts.TemplateForm
Set the multiValues
setMultiValues(String, String[]) - Method in class org.intermine.web.struts.TemplateForm
Set a multiselect attribute value
setName(String) - Method in class org.intermine.api.beans.ObjectDetails
 
setName(String) - Method in class org.intermine.api.profile.InterMineBag
Set the value of name
setName(String) - Method in class org.intermine.api.template.ApiTemplate
 
setName(String) - Method in class org.intermine.bio.chado.ChadoCVTerm
Set the name of this term.
setName(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setName(String) - Method in class org.intermine.bio.io.bed.BEDRecord
 
setName(String) - Method in class org.intermine.bio.io.gaf.GAFRecord
 
setName(String) - Method in class org.intermine.bio.ontology.OboTypeDefinition
 
setName(String) - Method in class org.intermine.task.project.Source
Set the name of this Source.
setName(String) - Method in class org.intermine.task.project.UserProperty
Set the name
setName(String) - Method in class org.intermine.template.TemplateQuery
Sets the query short name.
setName(String) - Method in class org.intermine.web.logic.aspects.Aspect
Set the data set name.
setName(String) - Method in class org.intermine.web.logic.aspects.AspectSource
Set the source name.
setName(String) - Method in class org.intermine.web.logic.template.TemplateResultInput
Sets template name.
setName(String) - Method in class org.intermine.web.struts.ContactForm
 
setName(String) - Method in class org.intermine.web.struts.TemplateForm
Set the template name.
setName(String) - Method in class org.intermine.web.struts.TemplateSettingsForm
 
setName(String) - Method in class org.intermine.webservice.client.services.TemplateService.TemplateRequest
Sets the name of the template to be used.
setName(String) - Method in class org.intermine.xml.full.Attribute
Set the name of this field
setName(String) - Method in class org.intermine.xml.full.Reference
Set the name of this field
setName(String) - Method in class org.intermine.xml.full.ReferenceList
Set the name of this field.
setNameSource(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
 
setNamespace(String) - Method in class org.intermine.bio.ontology.OboTerm
Set the namespace attribute.
setNameSpace(String) - Method in class org.intermine.webservice.server.WebService
Set the default name-space for configuration property look-ups.
setNewBagName(String) - Method in class org.intermine.api.bag.operations.BagOperation
 
setNewBagName(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm
Set the bag name.
setNewBagName(String) - Method in class org.intermine.web.struts.ModifyBagForm
Set the new bag name.
setNewBagName(String) - Method in class org.intermine.web.struts.SaveBagForm
Sets the value of newBagName
setNewBagType(String) - Method in class org.intermine.web.struts.TriageBagForm
Set the new bag name.
setNewpassword(String) - Method in class org.intermine.web.struts.ChangePasswordForm
The new password
setNewpassword(String) - Method in class org.intermine.web.struts.PasswordResetForm
Sets the value of newpassword.
setNewpassword2(String) - Method in class org.intermine.web.struts.ChangePasswordForm
New password verification
setNewpassword2(String) - Method in class org.intermine.web.struts.PasswordResetForm
Sets the value of newpassword2.
setNextEnabled(boolean) - Method in class org.intermine.web.tags.table.NavigationBarTag
 
setNextUniqueNumber(long) - Static method in class org.intermine.metadata.StringUtil
Sets the number that is used to generate the next uniqueString.
setNoCache(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets that the result must not be cached.
setNoCacheEnforced(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets enforced no-cache headers to completely disable cache for this response.
setNoExplain() - Method in interface org.intermine.objectstore.proxy.LazyCollection
Sets this LazyCollection to bypass the explain check in ObjectStore.execute().
setNoExplain() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Sets this LazyCollection to bypass the explain check in ObjectStore.execute().
setNoExplain() - Method in class org.intermine.objectstore.query.Results
Sets this Results object to bypass the explain check in ObjectStore.execute().
setNoFollow(boolean) - Method in class org.intermine.task.Dependencies
Set whether or not to visit dependencies of dependencies.
setNoOptimise() - Method in interface org.intermine.objectstore.proxy.LazyCollection
Sets this LazyCollection to bypass the optimiser
setNoOptimise() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Sets this LazyCollection to bypass the optimiser
setNoOptimise() - Method in class org.intermine.objectstore.query.Results
Sets this Results object to bypass the optimiser.
setNoPrefetch() - Method in class org.intermine.objectstore.query.Results
Tells this Results object to never do any background prefetching.
setNoResultsMessage(String) - Method in class org.intermine.web.tags.table.TableTag
 
setNotAnalysed(int) - Method in class org.intermine.web.logic.widget.HTMLWidget
 
setNotAnalysed(int) - Method in class org.intermine.web.logic.widget.Widget
 
setNullConstraint(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Set the null/not null constraint.
setNullConstraint(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm
Set the nullConstraint
setNullConstraint(String, String) - Method in class org.intermine.web.struts.TemplateForm
Set a nullConstraint
setNumberOfMainTitlesToShow(Integer) - Method in class org.intermine.web.logic.config.HeaderConfigTitle
How many main titles to show in the main title
setNumberOpt(String) - Method in class org.intermine.web.struts.WidgetForm
 
setOAuth2Providers(ServletContext, Set<String>) - Static method in class org.intermine.web.logic.session.SessionMethods
Set the set of supported OAuth2 providers to use.
setoBJECT(String, ObjectStore) - Method in interface org.intermine.model.InterMineObject
Sets the values of the fields to the values in the given NotXml.
setoBJECT(String[], ObjectStore) - Method in interface org.intermine.model.InterMineObject
Sets the values of the fields to the values in the given split NotXml.
setoBJECT(String, ObjectStore) - Method in class org.intermine.objectstore.proxy.ProxyReference
Sets the values of the fields to the values in the given NotXml.
setoBJECT(String[], ObjectStore) - Method in class org.intermine.objectstore.proxy.ProxyReference
Sets the values of the fields to the values in the given split NotXml.
setObjectId(Integer) - Method in class org.intermine.web.logic.results.InlineResultsTableRow
Set imObj ID for the object (taken from the first valid imObj id for this row)
setObjects(Set<ObjectDetails>) - Method in class org.intermine.api.beans.PartnerLink
 
setObjectStore(ObjectStore) - Method in class org.intermine.objectstore.translating.Translator
Set this Translator's ObjectStore.
setObjectStore(ObjectStore) - Method in class org.intermine.task.CreateIndexesTask
Set the ObjectStore to use.
setObjectStore(ObjectStore) - Method in class org.intermine.web.task.CreateSearchIndexTask
Set the object store.
setObjectStoreAlias(String) - Method in class org.intermine.web.task.EvictOrphansTask
Bean-style setter so that any can do its stuff.
setObjectStoreWriter(String) - Method in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask
Sets the value of objectStoreWriter
setObjectStoreWriter(String) - Method in class org.intermine.bio.postprocess.PostProcessOperationsTask
Sets the value of objectStoreWriter
setOboRelations(List<OboRelation>) - Method in class org.intermine.bio.dataconversion.OboConverter
 
setOboTerms(Collection<OboTerm>) - Method in class org.intermine.bio.dataconversion.OboConverter
 
setObsolete(boolean) - Method in class org.intermine.bio.ontology.OboTerm
Set the obsolete flag for this OboTerm as read from an OBO file.
setOldModelLocation(String) - Method in class org.intermine.web.task.ModelUpdateTask
Set the location of the previous model.
setOldpassword(String) - Method in class org.intermine.web.struts.ChangePasswordForm
The old password
setOmit(String) - Method in class org.intermine.task.InheritanceDotTask
Set a list of classnames to omit from the graph
setOnClick(String) - Method in class org.intermine.web.tags.disclosure.DisclosureTag
 
setOntologyName(String) - Method in class org.intermine.bio.task.OboConverterTask
Set the name of the ontology
setOntologyPrefix(String) - Method in class org.intermine.bio.dataconversion.OboConverter
The prefix of ontology terms to be processed.
setOpenByDefault(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
Set whether this field should be uncollapsed if sectionOnRight is true.
setOpened(boolean) - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Sets new state of disclosure.
setOpenIdProviders(ServletContext, Set<String>) - Static method in class org.intermine.web.logic.session.SessionMethods
Set the set of supported Open-ID providers to use.
setOperation(String) - Method in class org.intermine.bio.postprocess.PostProcessOperationsTask
Sets the value of operation
setOperationButton(String) - Method in class org.intermine.web.struts.SaveBagForm
 
setOperator(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Set the operator, "and" or "or"
setOptions(String) - Method in class org.intermine.web.task.KeyStoreTask
Bean-style setter for optionsFile, as per ant spec.
setOptionsTileName(String) - Method in class org.intermine.web.logic.config.TableExportConfig
Set the optionsTileName of this TableExportConfig
setOrCheckClass(ResultElement, Path, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Set the class, or if one is already set on the map, check that this one is valid for it.
setOrCheckClassAndId(ResultElement, Path, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Sets the basic information (class and objectId) on the jsonMap provided.
setOrCheckId(ResultElement, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Set the id, or if one is already set, check that it matches the one on the map.
setOrganism(String) - Method in class org.intermine.bio.dataconversion.EnsemblGwasDbConverter
Set the organism to load
setOrganism(String) - Method in class org.intermine.bio.dataconversion.EnsemblSnpDbConverter
Set the organism to load
setOrganism(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Set organism item, this is global across record handler and final
setOrganism(String) - Method in class org.intermine.bio.web.model.GenomicRegion
 
setOrganism(String) - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
 
setOrganisms(String) - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
Set the taxon ids to use when creating the Organism Item for the new features.
setOrganisms(String) - Method in class org.intermine.bio.dataconversion.UniprotFilterTask
A space separated list of NCBI taxon ids to include in the filter output.
setOrganisms(String) - Method in class org.intermine.bio.postprocess.IntronUtil
Set a comma separated list of taxon ids to create introns for.
setOrganisms(Set<Integer>) - Method in class org.intermine.bio.web.struts.GFF3ExportForm
Set the organisms
setOrganName(String) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList
 
setOrgansimString(String) - Method in class org.intermine.bio.web.struts.BEDExportForm
 
setOrgList(String) - Method in class org.intermine.bio.web.model.OrganismInfo
 
setOrgName(String) - Method in class org.intermine.bio.web.model.ChromosomeInfo
 
setOrgName(String) - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint
 
setOrgTaxonId(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
Set the organism taxon id
setOriginalConstraint(PathConstraint) - Method in class org.intermine.web.logic.query.DisplayConstraint
 
setOrthodbHomologues(String) - Method in class org.intermine.bio.dataconversion.OrthodbConverter
Sets the list of taxonIds of homologues that should be processed.
setOrthodbOrganisms(String) - Method in class org.intermine.bio.dataconversion.OrthodbConverter
Sets the list of taxonIds that should be processed.
setOsAlias(String) - Method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever
Set the ObjectStore alias.
setOsAlias(String) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
Set the ObjectStore alias.
setOsAlias(String) - Method in class org.intermine.bio.dataconversion.Protein2iprConverter
Set the ObjectStore alias.
setOsAlias(String) - Method in class org.intermine.task.StaticMethodTask
Set the os alias.
setOSAlias(String) - Method in class org.intermine.web.task.CreateSearchIndexTask
Set the alias of the main object store.
setOSAlias(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
Set the alias of the main object store.
setOSAlias(String) - Method in class org.intermine.web.task.LoadBagValuesTask
Set the alias of the main object store.
setOSAlias(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
Set the alias of the main object store.
setOSAlias(String) - Method in class org.intermine.web.task.ModelUpdateTask
Set the alias of the main object store.
setOSAlias(String) - Method in class org.intermine.web.task.ProfileReadTask
Set the alias of the main object store.
setOSAlias(String) - Method in class org.intermine.web.task.ProfileWriteTask
Set the alias of the main object store.
setOSAlias(String) - Method in class org.intermine.web.task.UpdateListTablesTask
Set the alias of the main object store.
setOsb(ObjectStoreBag) - Method in class org.intermine.api.profile.InterMineBag
Sets the ObjectStoreBag.
setOsName(String) - Method in class org.intermine.bio.task.OboConverterTask
Set the objectstore name
setOsName(String) - Method in class org.intermine.objectstore.intermine.TorqueModelOutputTask
Set the ObjectStore for which to generate the data.
setOsName(String) - Method in class org.intermine.task.AnalyseDbTask
Set the database alias
setOsName(String) - Method in class org.intermine.task.BuildDbTask
Sets the objectstore
setOsName(String) - Method in class org.intermine.task.ConverterTask
Set the objectstore name
setOsName(String) - Method in class org.intermine.task.PostProcessorTask
Set the ObjectStore alias.
setOsName(String) - Method in class org.intermine.task.RetrieveMetadataTask
Sets the os alias
setOsName(String) - Method in class org.intermine.task.StoreMetadataTask
Sets the database alias
setOut(OutputStream) - Method in class org.intermine.web.task.KeyStoreTask
Set the output handler.
setOuterInSummary(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
 
setOuterJoin(boolean) - Method in class org.intermine.pathquery.Node
Sets whether this should be an outer join.
setOuterJoins(PathQuery, String) - Method in class org.intermine.pathquery.PathQueryHandler
Given a path that may contain ':' characters to represent outer joins, find each : separated segment and set the status for that join to OUTER.
setOuterJoinStatus(String, OuterJoinStatus) - Method in class org.intermine.pathquery.PathQuery
Sets the outer join status of the last part of a given path in this query.
setOutputFile(String) - Method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever
Set the output file name
setOutputFile(String) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
Set the output file name
setOutputFile(File) - Method in class org.intermine.bio.postprocess.PostProcessOperationsTask
Sets the value of outputFile
setOutputFile(File) - Method in class org.intermine.bio.task.SOClassNameMapMakerTask
Sets the value of outputFile.
setOutputFile(File) - Method in class org.intermine.bio.task.SOToModelTask
Set the output file to write generated additions XML to.
setOutputFile(File) - Method in class org.intermine.task.AcceptanceTestTask
Set the File to write output to
setOutputFile(File) - Method in class org.intermine.task.ModelMergerTask
Path of file to write resulting model to.
setOutputFile(File) - Method in class org.intermine.task.SummariseObjectStoreTask
Set the name of the file to write the summary into
setOverwriting(boolean) - Method in class org.intermine.web.struts.ImportTagsForm
Set the overwriting flag.
setOverwriting(boolean) - Method in class org.intermine.web.struts.TemplatesImportForm
Set the overwriting flag.
setPackageName(String) - Method in class org.intermine.objectstore.query.iql.IqlQuery
Set the package name NOTE: this method is merely here to make this a Bean.
setPackageName(String) - Method in class org.intermine.task.InheritanceDotTask
Set the package name to describe.
setPage(Page) - Method in interface org.intermine.webservice.client.core.Request
Set the page for this request.
setPage(Page) - Method in class org.intermine.webservice.client.core.RequestImpl
Specify what section of the result set you wish to retrieve.
setPageAndPageSize(int, int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Set the page size and page together.
setPageName(String) - Method in class org.intermine.web.struts.ModifyBagForm
 
setPageName(String) - Method in class org.intermine.web.struts.ModifyTemplateForm
 
setPageSize(int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Set the page size of the table
setPageSize(String) - Method in class org.intermine.web.struts.ChangeTableSizeForm
Set the page size
setPageSize(Integer) - Method in class org.intermine.web.tags.table.NavigationBarTag
 
setPantherHomologues(String) - Method in class org.intermine.bio.dataconversion.PantherConverter
Sets the list of taxonIds of homologues that should be processed.
setPantherOrganisms(String) - Method in class org.intermine.bio.dataconversion.PantherConverter
Sets the list of taxonIds that should be processed.
setParameter(String, String) - Method in interface org.intermine.webservice.client.core.Request
Sets parameter
setParameter(String, String) - Method in class org.intermine.webservice.client.core.RequestImpl
Sets parameter
setParameterName(String) - Method in class org.intermine.web.logic.template.ConstraintInput
 
setParameters(List<?>) - Method in class org.intermine.objectstore.query.iql.IqlQuery
Set the parameters
setParameters(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
A JSON string representing custom parameters for this displayer.
setParentTermId(String) - Method in class org.intermine.bio.ontology.OboRelation
 
setPassword(String, String) - Method in class org.intermine.api.profile.ProfileManager
Change a user's password A check should be made prior to this call to ensure a Profile exists
setPassword(String) - Method in class org.intermine.web.struts.CreateAccountForm
 
setPassword(String) - Method in class org.intermine.web.struts.LoginForm
Sets the value of password
setPassword(String) - Method in class org.intermine.webservice.server.WebServiceInput
 
setPassword2(String) - Method in class org.intermine.web.struts.CreateAccountForm
 
setPath(String) - Method in class org.intermine.web.logic.config.InlineListConfig
Path set from WebConfig, ie "probeSets.primaryIdentifier"
setPath(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of path
setPathConstraints(String, List<? super PathConstraint>) - Static method in class org.intermine.web.logic.widget.config.WidgetConfig
Turn a string representing a set of constraints into a list of constraints.
setPathId(String) - Method in class org.intermine.web.logic.template.ConstraintInput
 
setPathQuery(PathQuery) - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
 
setPathsString(String) - Method in class org.intermine.web.struts.TableExportForm
Set the paths string
setPathStrings(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
setPdbOrganisms(String) - Method in class org.intermine.bio.dataconversion.PdbConverter
Sets the list of taxonIds that should be imported if using split input files.
setPerm(String) - Method in class org.intermine.task.GrantTask
The permission to grant: SELECT, INSERT, UPDATE, DELETE, RULE, REFERENCES, TRIGGER, ALL
setPlacement(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Set the data category name under which this displayer should appear.
setPlainTextContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets plain text content type.
setPlainTextHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets response header and content type for plain text output.
setPopulationBagName(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
Set the bag's name for reference population
setPreference(Profile, String, String) - Method in class org.intermine.api.profile.PreferencesManager
 
SetPreferencesService - Class in org.intermine.webservice.server.user
A service to set one or more preferences for a user.
SetPreferencesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.SetPreferencesService
 
setPrefix(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
Only used for MGI for now
setPrimaryIdentifier(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setProcessors(String) - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
Set the class names of the ChadoProcessors to run.
setProfile(HttpSession, Profile) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the user profile in the session.
setProfileId(Integer) - Method in class org.intermine.api.profile.InterMineBag
Sets the profileId - moves this bag from one profile to another.
setProjectXml(File) - Method in class org.intermine.task.Integrate
Set the project.xml to use for this Task.
setProjectXml(File) - Method in class org.intermine.task.MergeSourceModelsTask
Set the project.xml file to use when post-processing.
setProjectXml(File) - Method in class org.intermine.task.PostProcessTask
Set the project.xml file to use when post-processing.
setPropertiesOrigins(ServletContext, Map<String, List<String>>) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the origins of the web properties on the servlet context.
setProperty(String) - Method in class org.intermine.task.FileName
 
setProperty(String) - Method in class org.intermine.task.ReadResourceTask
The Ant property to set.
setProperty(String, String) - Method in class org.intermine.webservice.server.jbrowse.util.NameSpacedProperties
 
setPropertyName(String) - Method in class org.intermine.web.struts.EditPropertiesForm
Set the property name.
setPropertyValue(String) - Method in class org.intermine.web.struts.EditPropertiesForm
Set the value of the property
setPropName(String) - Method in class org.intermine.task.XPathSelect
Specify the property to set when the XPath expression matches.
setProtein2iprOrganisms(String) - Method in class org.intermine.bio.dataconversion.Protein2iprConverter
 
setProteinNames(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setPublication(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder
 
setPublicId(String) - Method in class org.intermine.webservice.server.lists.ListsServiceInput
Sets id of object.
setPubmedOrganisms(String) - Method in class org.intermine.bio.dataconversion.PubMedGeneConverter
Sets the list of taxonIds that should be imported
setPubs(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setPValue(String) - Method in class org.intermine.web.struts.WidgetForm
 
setQuery(String) - Method in class org.intermine.task.RunIqlQueryTask
An query string to execute, may be IQL or SQL by format parameter must be set correctly, richard
setQuery(HttpSession, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods
Set the current query on the session.
setQuery(String) - Method in class org.intermine.web.struts.QueryForm
 
setQueryBuilder(String) - Method in class org.intermine.web.struts.ImportQueriesForm
Set the queryBuilder field.
setQueryClass(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
If the name of a class is set will only load objects of that type.
setQueryInfo(PathQuery, ResultsInfo) - Method in class org.intermine.api.query.WebResultsExecutor
Sets a ResultsInfo entry in the infoCache for a given PathQuery.
setQueryName(String) - Method in class org.intermine.web.struts.SaveQueryForm
Set the query name
setQueryString(String) - Method in class org.intermine.objectstore.query.iql.IqlQuery
Set the query String NOTE: this method is merely here to make this a Bean.
setQueryXml(String) - Method in class org.intermine.webservice.client.services.QueryService.QueryRequest
Adds the query to be run.
setRangeConstraint(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Set the range constraint value.
setRangeLabel(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
Set the value of rangeLabel
setRangeOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
setReactomeOrganisms(String) - Method in class org.intermine.bio.dataconversion.ReactomeConverter
Sets the list of taxonIds that should be imported if using split input files.
setRedundant(boolean) - Method in class org.intermine.bio.ontology.OboRelation
 
setReference(String, String) - Method in class org.intermine.xml.full.Item
Add a reference to this item.
setReference(String, Item) - Method in class org.intermine.xml.full.Item
Add a reference that points to a particular item.
setRefId(String) - Method in class org.intermine.xml.full.Reference
Set the refId of this field
setRefIds(List<String>) - Method in class org.intermine.xml.full.ReferenceList
Set the references in this collection
setRegions(List<String>) - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo
 
setRelationship(OboTypeDefinition) - Method in class org.intermine.bio.ontology.OboRelation
 
setReplacesFields(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Set the comma separated list of field names that should not be displayed on the report page when this displayer is used.
setResource(String) - Method in class org.intermine.task.ReadResourceTask
Set the resource to search for.
setResponseHeader(HttpServletResponse, boolean) - Method in class org.intermine.web.logic.export.http.CSVHttpExporter
Sets header and content type of result in response.
setResponseHeader(HttpServletResponse, boolean) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter
Sets header and content type of result in response.
setResponseHeader(HttpServletResponse, boolean) - Method in class org.intermine.web.logic.export.http.TabHttpExporter
Sets header and content type of result in response.
setResultsTable(HttpSession, String, PagedTable) - Static method in class org.intermine.web.logic.session.SessionMethods
 
setRetryCount(int) - Method in class org.intermine.webservice.client.util.HttpConnection
Sets retry count.
setReturnToString(String) - Method in class org.intermine.web.struts.LoginForm
Sets the URL to return to if the login is successful.
setRowFormatter(RowFormatter) - Method in class org.intermine.webservice.server.output.FlatFileFormatter
Set the row formatter
setRows(int) - Method in class org.intermine.objectstore.query.ResultsInfo
Sets the estimated number of rows in the results.
setRows(List<List<String>>) - Method in class org.intermine.web.tags.table.TableTag
Set table rows.
setRowSpan(Integer) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
Set how many rows this identifier spans
setSavedTemplateQuery(SavedTemplateQuery) - Method in class org.intermine.api.template.ApiTemplate
Sets the saved template query object.
setSavePopulation(boolean) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
 
setSchemafile(String) - Method in class org.intermine.task.BuildDbTask
Adds the schemafile to be processed.
setScope(String) - Method in class org.intermine.web.struts.TemplateForm
Set the template scope.
setScore(int) - Method in class org.intermine.bio.io.bed.BEDRecord
 
setScore(int) - Method in class org.intermine.bio.io.gaf.GAFRecord
 
setSectionOnRight(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
Set whether this field should be rendered in its own section on the right side of the page.
setSectionTitle(String) - Method in class org.intermine.web.logic.config.FieldConfig
Set the section title (if sectionOnRight == true).
setSelectable(boolean) - Method in class org.intermine.api.results.Column
Sets the value of selectable
setSelected(boolean) - Method in class org.intermine.web.logic.query.MetadataNode
Sets the value of selected
setSelected(String[]) - Method in class org.intermine.web.struts.ModifyTemplateForm
Sets the selected templates
setSelected(String[]) - Method in class org.intermine.web.struts.WidgetForm
 
setSelectedBagOp(ConstraintOp) - Method in class org.intermine.web.logic.query.DisplayConstraint
Set the seletedBagOp
setSelectedBags(String[]) - Method in class org.intermine.web.struts.ModifyBagForm
Sets the selected bags
setSelectedBagValue(String) - Method in class org.intermine.web.logic.query.DisplayConstraint
Set the seletedBagValue returned bye the getSelectedValue if the bag is selected
setSelectedClass(String) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
setSelectedColumn(int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
setSelectedElements(String[]) - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Set the list of selectedElements
setSelectedExtraAttribute(String) - Method in class org.intermine.web.struts.WidgetForm
 
setSelectedObjects(String[]) - Method in class org.intermine.web.struts.BagUploadConfirmForm
Sets the ids of the selected objects - ie. those that should be included in the new bag
setSelectedObjects(String[]) - Method in class org.intermine.web.struts.SaveBagForm
Sets the selected objects
setSelectedQueries(String[]) - Method in class org.intermine.web.struts.ModifyQueryForm
Sets the selected queries
setSelectionIds(Map<Integer, String>) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
setSeqClsName(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
Set the sequenceClassName
setSeqDataSourceName(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
Set the seqDataSourceName
setSeqHandlerClassName(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
Set the name of GFF3SeqHandler to use when processing.
setSequence(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Set sequence item created for this record, should not be edited in handler.
setSequence(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setSequenceExportHeader(HttpServletResponse, boolean) - Static method in class org.intermine.bio.web.export.SequenceHttpExporter
Set response proper header.
setSequencePath(String) - Method in class org.intermine.bio.web.struts.SequenceExportForm
Sets the selected sequence path.
setSequenceType(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
Set the sequence type to be passed to the FASTA parser.
setSeriesLabels(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setSeriesPath(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setSeriesValues(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setServiceUrl(String) - Method in interface org.intermine.webservice.client.core.Request
Sets service URL.
setServiceUrl(String) - Method in class org.intermine.webservice.client.core.RequestImpl
Sets service URL.
setSession(HttpSession) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setShowExtraConstraint(boolean) - Method in class org.intermine.web.logic.query.DisplayConstraint
 
setShowIdentifier(Boolean) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
Set to show the identifier in this row
setShowImmediately(Boolean) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Set if we should display the displayer immediately
setShowInHeader(Boolean) - Method in class org.intermine.web.logic.config.InlineListConfig
Show this list in the header?
setShowInInlineCollection(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
Set the showInInlineCollection flag.
setShowInListAnalysisPreviewTable(Boolean) - Method in class org.intermine.web.logic.config.FieldConfig
Specify if we want to show this field for an object in list analysis page table preview
setShowInQB(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
Shall we show this field in a QueryBuilder?
setShowInResults(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
Set the showInResults flag.
setShowInSummary(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
Set the showInSummary flag.
setShowLinksToObjects(Boolean) - Method in class org.intermine.web.logic.config.InlineListConfig
Shall we show links to the objects's report pages?
setShowOnLeft(String) - Method in class org.intermine.web.logic.config.Displayer
 
setSingleton(boolean) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Sets whether the collection should be a singleton collection, or whether it should be a collection of ResultRows.
setSize(int) - Method in class org.intermine.webservice.server.lists.FlatListFormatter
 
setSize(int) - Method in class org.intermine.webservice.server.lists.HtmlListFormatter
 
setSize(int) - Method in class org.intermine.webservice.server.lists.JSONListFormatter
 
setSize(int) - Method in interface org.intermine.webservice.server.lists.ListFormatter
set the size of the list.
setSoFile(File) - Method in class org.intermine.bio.task.SOClassNameMapMakerTask
Sets the File containing the SO OBO data.
setSoFile(File) - Method in class org.intermine.bio.task.SOToModelTask
Sets the File containing the SO OBO data.
setSOTerm(DataConverter, Item, String, String) - Static method in class org.intermine.bio.dataconversion.BioStoreHook
For an item, set the SO term reference if one is not already set.
setSoTermListFile(File) - Method in class org.intermine.bio.task.SOToModelTask
Set the file containing a list of SO terms to be added to the data model.
setSource(Integer, String, Source) - Method in class org.intermine.dataloader.DataTracker
Set the Source for a field of an object in the database
setSource(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
Set the ObjectStore that is the data source.
setSource(Source) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Sets the source of the data, so we know what the primary keys are, and can fetch that extra data.
setSource(String) - Method in class org.intermine.task.Integrate
Set the source to integrate.
setSourceName(String) - Method in class org.intermine.bio.web.XRef
 
setSourceName(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
Set the source name, as used by primary key priority config.
setSourceName(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask
Set the source name, as used by primary key priority config.
setSourceName(String) - Method in class org.intermine.task.DirectDataLoaderTask
Set the source name, as used by primary key priority config.
setSourceName(String) - Method in class org.intermine.task.FullXmlConverterTask
Set the source name, as used by primary key priority config.
setSources(String) - Method in class org.intermine.bio.dataconversion.EnsemblSnpDbConverter
Optionally restrict the sources of SNPs to load by entries in source table, e.g. to dbSNP.
setSourceType(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
Set the source type, as used by primary key priority config.
setSourceType(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask
Set the source type, as used by primary key priority config.
setSourceType(String) - Method in class org.intermine.task.DirectDataLoaderTask
Set the source type, as used by primary key priority config.
setSrc(String) - Method in class org.intermine.web.logic.config.Displayer
Set the source of this displayer
setStart(int) - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
Set start value
setStart(Integer) - Method in class org.intermine.bio.web.model.GenomicRegion
 
setStart(long) - Method in class org.intermine.objectstore.query.ResultsInfo
Sets the estimated amount of time taken to produce the first row of the results.
setStart(int) - Method in class org.intermine.webservice.client.core.RequestImpl
Set the start parameter.
setStart(Integer) - Method in class org.intermine.webservice.server.WebServiceInput
Sets from which index should be results returned 1-based.
setStartClass(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setStartClassDisplay(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
setStartingPoints(String) - Method in class org.intermine.web.logic.aspects.Aspect
Set the starting point class names as a space seperated list.
setState(BagState) - Method in class org.intermine.api.profile.InterMineBag
Set bag state
setState(String, String) - Static method in class org.intermine.dwr.AjaxServices
Set state that should be saved during the session.
setState(String, Object) - Method in class org.intermine.web.logic.results.WebState
Set attribute.
setStoreHook(DataConverterStoreHook) - Method in class org.intermine.dataconversion.DataConverter
Set a hook for this converter that will be called just before each Item is stored.
setStrain(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
 
setStrand(String) - Method in class org.intermine.bio.io.bed.BEDRecord
 
setStrand(String) - Method in class org.intermine.bio.io.gaf.GAFRecord
 
setStrand(String) - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
Set strand value
setStyle(String) - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
Sets element style.
setStyleClass(String) - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
Sets css style class of element.
setSubclass(String) - Method in class org.intermine.web.logic.querybuilder.SummaryPath
Sets the subclass on this path.
setSubclassValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of subclassValue
setSubject(String) - Method in class org.intermine.web.struts.ContactForm
 
setSubject(String) - Method in class org.intermine.web.task.IssueTokenTask
Bean-style setter, as per the ant spec.
setSubTitle(String) - Method in class org.intermine.web.logic.aspects.Aspect
Set the subtitle.
setSubTitles(String) - Method in class org.intermine.web.logic.config.HeaderConfigTitle
Set subtitle(s) path(s) for the object, e.g.: organism.shortName => D. melanogaster
setSubType(String) - Method in class org.intermine.webservice.client.core.ContentType
 
setSummarise(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Set the summarise flag.
setSuperuser(boolean) - Method in class org.intermine.api.profile.Profile
Set the superuser flag and store it in userprofile database
setSuperuserPassword(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
Set the superuser's initial password.
setSuperUsers(String[]) - Method in class org.intermine.web.struts.ModifySuperUserForm
Sets the super users
setSwitchable(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
setSwitchOff(String, String) - Method in class org.intermine.web.struts.TemplateForm
Set the SwitchOff ability.
setSwitchOffAbility(PathConstraint, SwitchOffAbility) - Method in class org.intermine.template.TemplateQuery
Sets the sbitch-off-ability of a constraint.
setSwitchOffAbility(SwitchOffAbility) - Method in class org.intermine.web.logic.query.DisplayConstraint
Set the switchOffAbility
setTabContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets tab separated values content type.
setTabHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets response header and content type for tab separated values output.
setTable(String) - Method in class org.intermine.web.struts.TableExportForm
Set the table identifier to look up in the servlet context
setTableDisplayer(Displayer) - Method in class org.intermine.web.logic.config.Type
Set the table displayer for this Type
setTableid(String) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
setTag(Integer) - Method in class org.intermine.bio.web.model.GenomicRegion
 
setTagValues(Map<?, ?>) - Method in class org.intermine.bio.ontology.OboTerm
Sets the variable holding the raw tagValues that created this Term.
setTarget(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
Set the target ObjectStore alias
setTarget(String) - Method in class org.intermine.task.Dependencies
Set the ant target to execute on each dependency.
setTaxonId(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
 
setTaxonId(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
 
setTempdir(File) - Method in class org.intermine.task.BuildDbTask
Sets the directory for temporary files including sql output
setTemplateButton(String) - Method in class org.intermine.web.struts.ModifyTemplateForm
 
setTemplateFile(File) - Method in class org.intermine.task.CreatePropertiesFile
 
setTemplateLabel(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Set the template label.
setTemplateParameters(List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService.TemplateRequest
Set some template parameters.
setTemplatesummary(List<Object>) - Method in class org.intermine.web.logic.query.DisplayConstraint
 
setTemplatesXml(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
Set the templates xml file.
setTermClass(String) - Method in class org.intermine.bio.task.OboConverterTask
Set the term class name
setText(String) - Method in class org.intermine.web.logic.config.HeaderConfigLink
Set
setText(String) - Method in class org.intermine.web.struts.BuildBagForm
Set the query string
setTextToFind(String) - Method in class org.intermine.web.struts.FindInListForm
 
setTgtDir(File) - Method in class org.intermine.bio.dataconversion.UniprotFilterTask
Set the target directory
setTgtLocation(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Set the tgtLocation item for this record.
setTgtOrganism(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Get the tgtOrganism item to use in this handler
setTgtSequence(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
Set tgtSequence item created for this record, should not be edited in handler.
setThickEnd(int) - Method in class org.intermine.bio.io.bed.BEDRecord
 
setThickEnd(int) - Method in class org.intermine.bio.io.gaf.GAFRecord
 
setThickStart(int) - Method in class org.intermine.bio.io.bed.BEDRecord
 
setThickStart(int) - Method in class org.intermine.bio.io.gaf.GAFRecord
 
setThreshold(int) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
This sets the threshold above which a temp table will be used for deletes.
setTileName(String) - Method in class org.intermine.web.logic.aspects.Aspect
Set the name of the tile/page to embed in the centre of the data set homepage.
setTimeLimit(long) - Method in class org.intermine.sql.precompute.QueryOptimiserContext
Sets the optimiser's maximum effort time, in milliseconds.
setTimeout(int) - Method in class org.intermine.webservice.client.util.HttpConnection
Sets timeout.
settings - Variable in class org.intermine.sql.Database
 
setTitle(String) - Method in class org.intermine.api.template.ApiTemplate
 
setTitle(String) - Method in class org.intermine.pathquery.PathQuery
Sets the name of the query.
setTitle(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setTitle(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setTitle(String) - Method in class org.intermine.web.struts.TemplateSettingsForm
Set the title
setToFile(File) - Method in class org.intermine.task.CreatePropertiesFile
 
setToggledElements(Map<String, Boolean>) - Method in class org.intermine.web.logic.results.WebState
Sets map of ids and its state.
setToken(String) - Method in class org.intermine.web.struts.PasswordResetForm
Sets the value of token.
setToken(String) - Method in class org.intermine.web.task.VerifyTokenTask
Bean-style setter for token, as per ant spec.
setTrackDescription(String) - Method in class org.intermine.bio.web.struts.BEDExportForm
 
setTrackQueue(Queue<Track>) - Method in class org.intermine.api.tracker.AbstractTracker
Set the queue of tracks
setTransitive(boolean) - Method in class org.intermine.bio.ontology.OboTypeDefinition
 
setTransitiveOver(List<String>) - Method in class org.intermine.bio.ontology.OboTypeDefinition
 
setTreatColNames(boolean) - Method in class org.intermine.web.tags.table.TableTag
 
setTreefamHomologues(String) - Method in class org.intermine.bio.dataconversion.TreefamConverter
Sets the list of taxonIds of homologues that should be processed.
setTreefamOrganisms(String) - Method in class org.intermine.bio.dataconversion.TreefamConverter
Sets the list of taxonIds that should be processed.
setType(String) - Method in class org.intermine.api.beans.ObjectDetails
 
setType(String) - Method in class org.intermine.api.profile.InterMineBag
 
setType(String) - Method in class org.intermine.bio.io.gff3.GFF3Record
Set the type of this record.
setType(String) - Method in class org.intermine.pathquery.Node
Set the value of type
setType(String) - Method in class org.intermine.task.Dependencies
Set the dependency type.
setType(String) - Method in class org.intermine.task.ModelOutputTask
Set the type of model output required.
setType(String) - Method in class org.intermine.task.project.Project
Set the type of this project.
setType(String) - Method in class org.intermine.task.project.Source
Set the name of this Source.
setType(String) - Method in class org.intermine.web.logic.query.MetadataNode
Set the value of type
setType(String) - Method in class org.intermine.web.struts.BuildBagForm
Set the bag type
setType(String) - Method in class org.intermine.web.struts.TableExportForm
Set the type
setType(String) - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Sets type of tag.
setType(String) - Method in class org.intermine.webservice.client.core.ContentType
Sets main content type.
setType(Request.RequestType) - Method in interface org.intermine.webservice.client.core.Request
 
setType(Request.RequestType) - Method in class org.intermine.webservice.client.core.RequestImpl
setType(String) - Method in class org.intermine.webservice.server.lists.ListsServiceInput
Sets object type.
setTypeClass(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setTypes(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Set the types this displayer should be used for as a comma separated list of unqualified class names.
setUcscCompatibleCheck(String) - Method in class org.intermine.bio.web.struts.BEDExportForm
 
setUniprot(String) - Method in class org.intermine.bio.util.OrganismData
 
setUniprotOrganisms(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter
Sets the list of taxonIds that should be imported if using split input files.
setUniqueIdentifier(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
 
setUp() - Method in class org.intermine.task.CreateIndexesTask
Sets up the instance variables
setupDatabase(Connection) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Sets up the database for storing precomputed tables
setupFieldValues() - Method in class org.intermine.web.logic.results.ReportObject
Setup fieldValues HashMap
setUpPermission(InterMineAPI, ProfileManager.ApiPermission) - Static method in class org.intermine.web.logic.profile.LoginHandler
Does whatever needs to be done to a permissions object to get it ready for a life cyle in a web service request.
setUpProfile(HttpSession, String, String) - Static method in class org.intermine.web.logic.profile.LoginHandler
Initialises a profile for the current user based on their user name and password.
setUpProfile(HttpSession, Profile) - Static method in class org.intermine.web.logic.profile.LoginHandler
Sets up a profile ready for a session in InterMine.
setupWebData() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
To call the queryOrganismAndSequenceFeatureTypes method in GenomicRegionSearchQueryRunner.
setUrl(String) - Method in class org.intermine.bio.task.OboConverterTask
Set the url for the source of the ontology
setUrl(String) - Method in class org.intermine.bio.web.XRef
 
setUrl(String) - Method in class org.intermine.web.logic.aspects.AspectSource
Set the URL to source website.
setUrl(String) - Method in class org.intermine.web.logic.config.HeaderConfigLink
Set
setUrl(String) - Method in interface org.intermine.webservice.client.core.Request
Sets whole request URL.
setUrl(String) - Method in class org.intermine.webservice.client.core.RequestImpl
Sets whole request URL.
setUseBagConstraint(String, boolean) - Method in class org.intermine.web.struts.TemplateForm
Set value of useBagConstraint for given constraint key.
setUseJoin(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
setUser(String) - Method in class org.intermine.task.GrantTask
Set user to grant permissions to
setUserId(Integer) - Method in class org.intermine.api.profile.Profile
Set the userId
setUsername(String) - Method in class org.intermine.web.struts.CreateAccountForm
 
setUsername(String) - Method in class org.intermine.web.struts.LoginForm
Sets the value of username
setUsername(String) - Method in class org.intermine.web.struts.RequestPasswordForm
Sets the value of username
setUsername(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
Set the account name to laod template to.
setUsername(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
Set the account name to load template to.
setUsername(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Set the account name to laod template to.
setUserName(String) - Method in class org.intermine.webservice.server.WebServiceInput
 
setUserProfileAlias(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.LoadBagValuesTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.ModelUpdateTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.ProfileReadTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.ProfileWriteTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.TemplateTrackReadTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.TemplateTrackWriteTask
Set the alias of the userprofile database.
setUserProfileAlias(String) - Method in class org.intermine.web.task.UpdateListTablesTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.UpdateTrackTableTask
Set the alias of the userprofile object store.
setValue(String) - Method in class org.intermine.task.project.UserProperty
Set the property value
setValue(String) - Method in class org.intermine.web.logic.template.ConstraintInput
Sets constraint value.
setValue(B) - Method in class org.intermine.webservice.server.core.Pair
 
setValue(String) - Method in class org.intermine.xml.full.Attribute
Set the value of this field
setVar(String) - Method in class org.intermine.task.SetDeployURL
 
setVcfDataSetName(String) - Method in class org.intermine.bio.dataconversion.VcfLoaderTask
Sets the data set, e.g.
setVcfDataSourceName(String) - Method in class org.intermine.bio.dataconversion.VcfLoaderTask
Sets the data source, e.g.
setVcfTaxonId(String) - Method in class org.intermine.bio.dataconversion.VcfLoaderTask
Sets the taxon ID for features in this file.
setVerboseQueryLog(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Sets the verboseQueryLog configuration option.
setVerboseQueryLog(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Sets the verboseQueryLog configuration option.
setView(String) - Method in class org.intermine.web.struts.TemplateForm
Set the selected alternative view name.
setViews(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setVisible(boolean) - Method in class org.intermine.api.results.Column
Sets the value of visible
setWebConfig(ServletContext, WebConfig) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the WebConfig into the ServletContext.
setWebConfig(WebConfig) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
setWebProperties(ServletContext, Properties) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the web properties in the session.
setWhichInput(String) - Method in class org.intermine.web.struts.BuildBagForm
Set the method the user used to upload her bag.
setWidgetid(String) - Method in class org.intermine.web.struts.WidgetForm
 
setWidgets(LinkedList) - Method in class org.intermine.web.logic.config.Type
 
setWidgetTitle(String) - Method in class org.intermine.web.struts.WidgetForm
used on results page for description: "results for widget XYZ"
setWriter(PrintWriter) - Method in class org.intermine.webservice.server.output.StreamedOutput
Sets associated writer
setXml(String) - Method in class org.intermine.web.struts.ImportTagsForm
Set the xml.
setXml(String) - Method in class org.intermine.web.struts.ImportXMLForm
Set the xml.
setXml(String) - Method in class org.intermine.webservice.server.query.result.QueryResultInput
Sets xml query string.
setXMLContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets XML content type.
setXMLFormat() - Method in class org.intermine.webservice.client.core.RequestImpl
Set the format as XML format.
setXMLHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets response header and content type for XML output.
setXmlResource(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask
Set XML resource name (to load data from classloader).
setXmlResource(String) - Method in class org.intermine.task.FullXmlConverterTask
Set XML resource name (to load data from classloader).
setXref(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
 
ShadowClass - Interface in org.intermine.model
A root interface for all shadow classes for performance.
shareBagWithUser(String, String, String) - Method in class org.intermine.api.bag.BagManager
Share the bag given in input with the user which userName input
shareBagWithUser(InterMineBag, Profile) - Method in class org.intermine.api.bag.BagManager
Let the recipient gain access to this bag in future uses of the application.
shareBagWithUser(InterMineBag, String) - Method in class org.intermine.api.bag.SharedBagManager
Share the bag given in input with user which userName is given in input
shareBagWithUser(String, String, String) - Method in class org.intermine.api.bag.SharedBagManager
Share the bag given in input with user which userName is given in input To be used ONLY when deserialising the user-profile from XML.
SHARED_BAGS - Static variable in class org.intermine.api.bag.SharedBagManager
the table name
SharedBagBinding - Class in org.intermine.api.xml
Parse the shared bags in XML format
SharedBagBinding() - Constructor for class org.intermine.api.xml.SharedBagBinding
 
SharedBagHandler - Class in org.intermine.api.xml
Handle parsing of shared bags
SharedBagHandler(List<Map<String, String>>) - Constructor for class org.intermine.api.xml.SharedBagHandler
Constructor
SharedBagManager - Class in org.intermine.api.bag
Singleton manager class for shared bags.
SharingBagUsersController - Class in org.intermine.web.struts
Controller for the inline tag editing tile
SharingBagUsersController() - Constructor for class org.intermine.web.struts.SharingBagUsersController
 
SharingInvite - Class in org.intermine.api.bag
A representation of an invitation to share a resource.
SharingInvite(InterMineBag, String) - Constructor for class org.intermine.api.bag.SharingInvite
Constructor.
SharingInvite(InterMineBag, String, String) - Constructor for class org.intermine.api.bag.SharingInvite
Constructor.
SharingInvite(InterMineBag, String, String, Date, Date, Boolean) - Constructor for class org.intermine.api.bag.SharingInvite
Constructor.
SharingInvite.IntermediateRepresentation - Class in org.intermine.api.bag
A structure for holding data we read from the DB.
SharingInvite.IntermediateRepresentation() - Constructor for class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
SharingInvite.NotFoundException - Exception in org.intermine.api.bag
Exception thrown when we can't find a shared invitation.
shortName - Variable in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder
 
shouldCancelQuery() - Method in interface org.intermine.web.logic.query.QueryMonitor
Called intermittently while a query is run providing an opportunity to cancel the query.
shouldCancelQuery() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Return true if tickle has not been called in a period of time greater than the timeout value.
shouldSavePopulation() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
showColumn(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction
Deprecated.
as we don't hide columns any more
shuffle(Map<String, V>, int) - Static method in class org.intermine.web.logic.WebUtil
takes a map and puts it in random order also shortens the list to be map.size() = max
shutdown() - Method in class org.intermine.api.tracker.TrackerDelegate
Called from ShutdownHook.
shutdown() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Called by the ShutdownHook on shutdown.
shutdown() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Called by the StatsShutdownHook on shutdown
shutdown() - Method in class org.intermine.sql.Database
Logs stuff
shutdown() - Method in interface org.intermine.util.Shutdownable
Shuts down an instance.
shutdown() - Static method in class org.intermine.util.ShutdownHook
Performs the shutdown.
shutdown() - Method in class org.intermine.web.context.InterMineContext
Send the signal that shutdown is happening - try and release resources.
Shutdownable - Interface in org.intermine.util
An interface for any object that can be shut down by the ShutdownHook.
ShutdownHook - Class in org.intermine.util
This class provides a "shutdown" service to other classes.
SimpleConstraint - Class in org.intermine.objectstore.query
Represents a constraint between two QueryEvaluable types.
SimpleConstraint(QueryEvaluable, ConstraintOp, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.SimpleConstraint
Construct a Constraint.
SimpleConstraint(QueryEvaluable, ConstraintOp) - Constructor for class org.intermine.objectstore.query.SimpleConstraint
Construct a Constraint.
simpleConstraintToString(SqlGenerator.State, StringBuffer, SimpleConstraint, Query) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a SimpleConstraint object into a String suitable for putting in an SQL query.
simpleCreateObject(Class<C>) - Static method in class org.intermine.util.DynamicUtil
Create a new object given a class, which may be an interface.
SingleTemplateService - Class in org.intermine.webservice.server.template
Service that responds with a single template.
SingleTemplateService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.SingleTemplateService
 
SINGLETON - Static variable in class org.intermine.util.NullFirstComparator
Publicly-accessible instance
SingletonResults - Class in org.intermine.objectstore.query
This class is equivalent to a Result object with ResultRows consisting only of single items
SingletonResults(Query, ObjectStore, Map<Object, Integer>) - Constructor for class org.intermine.objectstore.query.SingletonResults
Constructor for a SingletonResults object
SingletonResults(ResultsBatches, boolean, boolean, boolean) - Constructor for class org.intermine.objectstore.query.SingletonResults
Constructor for a SingletonResults object, given a ResultsBatches object.
singletonResultsCache - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
size() - Method in class org.intermine.api.profile.StorableBag
Returns the number of elements in the bag.
size() - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
size() - Method in class org.intermine.api.results.WebResults
size() - Method in class org.intermine.api.search.SearchResults
 
size() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Gets the number of elements in this collection
size() - Method in class org.intermine.objectstore.query.Results
Gets the number of results rows in this Results object
size(boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches
Gets the number of results rows in this Results object.
SIZE - Static variable in class org.intermine.objectstore.query.ResultsInfo
Denotes that the result of getRows() is the known size of the results.
size() - Method in class org.intermine.util.AlwaysMap
size() - Method in class org.intermine.util.ConsistentSet
Return the number of elements in this Set.
size() - Method in class org.intermine.util.IdentityMap
size() - Method in class org.intermine.util.IntPresentSet
Returns the number of ints present.
size() - Method in class org.intermine.util.IntToIntMap
Returns the number of mappings to non-minus-one ints present.
size() - Method in class org.intermine.util.PseudoSet
size() - Method in class org.intermine.util.ReferenceMap
size - Variable in class org.intermine.web.logic.results.InlineResultsTable
 
size() - Method in class org.intermine.webservice.client.lists.ItemList
Synonym for getSize()
size() - Method in class org.intermine.webservice.client.results.JsonRow
 
size() - Method in class org.intermine.webservice.client.results.ResultRowList
 
sizeOfArray(Object[]) - Static method in class org.intermine.sql.writebatch.TableBatch
Calculates the size of an array, in bytes.
sizeOfList(List<Object[]>) - Static method in class org.intermine.sql.writebatch.TableBatch
Calculates the size of a List of arrays, in bytes.
SKELETON - Static variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
skeletons - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
 
SKIP_BUILDER_PARAMETER - Static variable in class org.intermine.web.struts.TemplateAction
Name of skipBuilder parameter
SnpToGeneDisplayer - Class in org.intermine.bio.web.displayer
SNPs to nearby Genes displayer for metabolicMine report page
SnpToGeneDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.SnpToGeneDisplayer
Construct with config and the InterMineAPI.
SO_CLASS_NAMES - Static variable in class org.intermine.bio.webservice.BioExportServlet
so class names
SOClassNameMapMakerTask - Class in org.intermine.bio.task
A Task that reads a SO OBO files and writes a file mapping SO term names to FlyMine class names.
SOClassNameMapMakerTask() - Constructor for class org.intermine.bio.task.SOClassNameMapMakerTask
Create a new SOClassNameMapMakerTask object.
SoftReferenceMap<K,V> - Class in org.intermine.util
This is a Map implementation designed specifically for people intending to create a cache.
SoftReferenceMap() - Constructor for class org.intermine.util.SoftReferenceMap
 
SortableMap<K extends java.lang.Comparable<K>,V extends java.lang.Comparable<V>> - Class in org.intermine.web.logic
SortableMap extends a LinkedHashMap with some useful sorting features.
SortableMap() - Constructor for class org.intermine.web.logic.SortableMap
Default constructor.
SortableMap(Map<K, V>) - Constructor for class org.intermine.web.logic.SortableMap
Create new SortableMap based on the given Map.
sortConstraints(List<PathConstraint>) - Method in class org.intermine.pathquery.PathQuery
A method to sort constraints by a given lists, provided to allow TemplateQuery to set a specific sort order that will be preserved in a round-trip to XML.
sortKeys() - Method in class org.intermine.web.logic.SortableMap
Sort this map ascending on keys in natural order (default).
sortKeys(boolean, boolean) - Method in class org.intermine.web.logic.SortableMap
Sort this map on keys.
sortMap(Map<String, BigDecimal>) - Static method in class org.intermine.web.logic.widget.ErrorCorrection
Sort the map by values.
sortValues() - Method in class org.intermine.web.logic.SortableMap
Sort this map ascending on values in natural order (default).
sortValues(boolean, boolean) - Method in class org.intermine.web.logic.SortableMap
Sort this map on values.
SOToModelTask - Class in org.intermine.bio.task
A Task that reads a SO OBO files and writes so_additions.xml
SOToModelTask() - Constructor for class org.intermine.bio.task.SOToModelTask
 
source - Variable in class org.intermine.dataloader.BatchingFetcher
 
SOURCE - Static variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
source - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
Source - Class in org.intermine.dataloader
Represents a data source, by name and skeleton status.
Source(String, String, boolean) - Constructor for class org.intermine.dataloader.Source
Create a new source object.
Source(String, String) - Constructor for class org.intermine.dataloader.Source
Create a new source object that isn't a skeleton.
Source(String, boolean) - Constructor for class org.intermine.dataloader.Source
Create a new source object with no type information.
Source(String) - Constructor for class org.intermine.dataloader.Source
Create a new source object with no type information that isn't a skeleton
Source - Class in org.intermine.task.project
A class to hold information about a source from a project.xml file.
Source() - Constructor for class org.intermine.task.project.Source
 
sourceKeys - Static variable in class org.intermine.dataloader.DataLoaderHelper
 
sourceName - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
sourceName - Variable in class org.intermine.dataloader.XmlDataLoaderTask
 
sourceName - Variable in class org.intermine.task.DirectDataLoaderTask
 
sourceName - Variable in class org.intermine.task.FullXmlConverterTask
 
SourcePriorityComparator - Class in org.intermine.dataloader
Comparator, that compares two InterMineObjects, with reference to a particular FieldDescriptor for priority.
SourcePriorityComparator(DataTracker, Class<? extends InterMineObject>, String, Source, InterMineObject, IntPresentSet, IntegrationWriterAbstractImpl, Source, Source, PriorityConfig) - Constructor for class org.intermine.dataloader.SourcePriorityComparator
Constructs a new Comparator for comparing objects for priority for a given field.
sourceToString(Source) - Method in class org.intermine.dataloader.DataTracker
Converts a Source to a source name.
sourceType - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
SPACE - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
SPACE - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
SPACE - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
 
SPACE - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
SPACE_SPLITTER - Static variable in class org.intermine.pathquery.PathQuery
A Pattern that finds spaces in a String.
split(String, String) - Static method in class org.intermine.metadata.StringUtil
Returns a list of tokens delimited by delim in String str.
split(List<? extends Collection<String>>) - Method in class org.intermine.pathquery.LogicExpression
Takes a List of collections of String variables and returns a List of the same length, containing sections of the LogicExpression with those variables in.
SPLITTER - Static variable in class org.intermine.objectstore.intermine.NotXmlParser
A Pattern that will find delimiters.
sqlCache - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
 
SqlGenerator - Class in org.intermine.objectstore.intermine
Code to generate an sql statement from a Query object.
SqlGenerator.State - Class in org.intermine.objectstore.intermine
Internal representation of the State of the query as it is built up.
SqlGenerator.State() - Constructor for class org.intermine.objectstore.intermine.SqlGenerator.State
Constructor
SQLOperation<T> - Class in org.intermine.objectstore.intermine
A functional interface (oh, please come Java 8 - you cannot come soon enough) to help manage out-of-control boilerplate-itis in SQL code.
SQLOperation() - Constructor for class org.intermine.objectstore.intermine.SQLOperation
 
SQLStringable - Interface in org.intermine.sql.query
An interface for all classes that implement the getSQLString method.
StandardHttpExporter - Class in org.intermine.web.logic.export.http
Abstract class implementing functionality common for exporters exporting table in simple format like comma separated format.
StandardHttpExporter() - Constructor for class org.intermine.web.logic.export.http.StandardHttpExporter
Constructor.
start - Variable in class org.intermine.dataconversion.FullXmlConverter
 
start - Variable in class org.intermine.objectstore.query.OverlapRange
 
start - Variable in class org.intermine.objectstore.query.ResultsInfo
 
start - Variable in class org.intermine.sql.precompute.BestQueryExplainer
 
start - Variable in class org.intermine.sql.query.ExplainResult
 
START_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Name of start parameter that determines index of first returned result.
START_PATHS - Static variable in class org.intermine.web.struts.InterMineRequestProcessor
Paths that can be used as initial pages ie. when there is no session.
startClass - Variable in class org.intermine.web.logic.widget.WidgetLdr
 
startContainsClass(String) - Method in class org.intermine.pathquery.Path
Return true if the first element in the path has the class given in input as type
startDocument() - Method in class org.intermine.webservice.server.ServiceListingHandler
 
startElement(String, String, String, Attributes) - Method in class org.intermine.api.bag.BagQueryHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.api.bag.InvitationHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.api.profile.PreferencesHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.api.profile.TagHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.api.tracker.xml.TrackManagerHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.api.xml.InterMineBagHandler
InvalidBag
startElement(String, String, String, Attributes) - Method in class org.intermine.api.xml.SavedQueryHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.api.xml.SharedBagHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.pathquery.PathQueryHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.template.xml.TemplateQueryHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.webservice.server.ServiceListingHandler
 
startElement(String, String, String, Attributes) - Method in class org.intermine.xml.full.FullHandler
startListening() - Method in class org.intermine.api.search.SearchRepository
Begin listening for events on the items of interest.
startPagedTableCount(PageTableQueryMonitor, HttpSession, MessageResources) - Static method in class org.intermine.web.logic.session.SessionMethods
Start a query running in the background that will return the row count of the collection.
startQuery(QueryMonitor, HttpSession, MessageResources, boolean, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods
Start the current query running in the background, then return.
startQueryCount(QueryCountQueryMonitor, HttpSession, MessageResources) - Static method in class org.intermine.web.logic.session.SessionMethods
Start a query running in the background that will return the row count of the query argument.
startQueryWithTimeout(HttpServletRequest, boolean, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods
Start the given query running in the background, then return, with a default timeout.
startTemplateBuild(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Put query builder in template building mode.
StaticMethodTask - Class in org.intermine.task
Given a class name and method name, just invokes a static method.
StaticMethodTask() - Constructor for class org.intermine.task.StaticMethodTask
 
stats - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
stats(Command) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
stats(Command) - Method in class org.intermine.webservice.server.jbrowse.genomic.Engine
 
statsBagTableTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
statsConTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
statsEstTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
statsExeTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
statsGenTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
statsOptTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
StatusDictionary - Class in org.intermine.webservice.server
HTTP status code dictionary.
STDDEV - Static variable in class org.intermine.objectstore.query.QueryFunction
Sample standard deviation of a number of rows
STDDEV - Static variable in class org.intermine.sql.query.Function
STDDEV operator - takes one operand
stm - Variable in class org.intermine.api.tracker.xml.TrackHandler
 
StockProcessor - Class in org.intermine.bio.dataconversion
A ChadoProcessor for the chado stock module.
StockProcessor(ChadoDBConverter) - Constructor for class org.intermine.bio.dataconversion.StockProcessor
Create a new ChadoProcessor
stop() - Method in class org.intermine.webservice.server.idresolution.JobJanitor
Let others tell us to stop.
stopListening() - Method in class org.intermine.api.search.SearchRepository
Stop listening for events
stopTemplateBuild(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Bring the query builder out of template building mode and discard any unfinished template building.
StorableBag - Class in org.intermine.api.profile
Base class for representations of user's collections of objects stored in a database.
StorableBag() - Constructor for class org.intermine.api.profile.StorableBag
 
store(Connection) - Method in interface org.intermine.api.tracker.track.Track
Save into the table the track object representing the user activity
store(Connection) - Method in class org.intermine.api.tracker.track.TrackAbstract
 
store(Item, int) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
Store the feature Item.
store(Item, int) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
Store the feature Item.
store(Item, int) - Method in class org.intermine.bio.dataconversion.WormBaseProcessor
Store the feature Item.
store(Item) - Method in class org.intermine.dataconversion.DataConverter
Store a single XML Item
store(ReferenceList, Integer) - Method in class org.intermine.dataconversion.DataConverter
Store a single XML ReferenceList
store(Attribute, Integer) - Method in class org.intermine.dataconversion.DataConverter
Store a single XML Attribute
store(Reference, Integer) - Method in class org.intermine.dataconversion.DataConverter
Store a single XML Reference
store(Collection<Item>) - Method in class org.intermine.dataconversion.DataConverter
Store a Collection of XMl Items
store(Item) - Method in interface org.intermine.dataconversion.ItemWriter
Stores the given Item and all its associated attributes, references, and referencelists.
store(ReferenceList, Integer) - Method in interface org.intermine.dataconversion.ItemWriter
Stores the given ReferenceList after setting its item id.
store(Reference, Integer) - Method in interface org.intermine.dataconversion.ItemWriter
Stores the given Reference after setting its item id.
store(Attribute, Integer) - Method in interface org.intermine.dataconversion.ItemWriter
Stores the given Attribute after setting its item id.
store(Item) - Method in class org.intermine.dataconversion.MockItemWriter
Stores the given Item and all its associated attributes, references, and referencelists.
store(ReferenceList, Integer) - Method in class org.intermine.dataconversion.MockItemWriter
Stores the given ReferenceList after setting its item id.
store(Reference, Integer) - Method in class org.intermine.dataconversion.MockItemWriter
Stores the given Reference after setting its item id.
store(Attribute, Integer) - Method in class org.intermine.dataconversion.MockItemWriter
Stores the given Attribute after setting its item id.
store(Item) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
Stores the given Item and all its associated attributes, references, and referencelists.
store(ReferenceList, Integer) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
Stores the given ReferenceList after setting its item id.
store(Reference, Integer) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
Stores the given Reference after setting its item id.
store(Attribute, Integer) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
Stores the given Attribute after setting its item id.
store(FastPathObject) - Method in class org.intermine.dataloader.DirectDataLoader
Store an object using the IntegrationWriter, buffering writes so that integration queries and database writes can be run in batches.
store(FastPathObject, Source, Source) - Method in interface org.intermine.dataloader.IntegrationWriter
Stores the given object in the objectstore.
store(FastPathObject, Source, Source) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Stores the given object in the objectstore.
store(FastPathObject, Source, Source, int) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Stores the given object in the objectstore.
store(Object) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Store an object in this ObjectStore, delegates to internal ObjectStoreWriter.
store(FastPathObject, Source, Source, int) - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Stores the given object in the objectstore.
store(Database, String, String) - Static method in class org.intermine.modelproduction.MetadataManager
Store a (key, value) pair in the metadata table of the database
store(Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Store an object in this ObjectStore.
store(Object) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Store an object in this ObjectStore.
storeAll() - Method in class org.intermine.bio.dataconversion.GFF3Converter
store all the items
storeAll(Collection<Item>) - Method in interface org.intermine.dataconversion.ItemWriter
Stores the given Collection of Items and all their associated attributes, references, and referencelists.
storeAll(Collection<Item>) - Method in class org.intermine.dataconversion.MockItemWriter
Stores the given Collection of Items and all their associated attributes, references, and referencelists.
storeAll(Collection<Item>) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
Stores the given Collection of Items and all their associated attributes, references, and referencelists.
storeBinary(Database, String, byte[]) - Static method in class org.intermine.modelproduction.MetadataManager
Store a binary (key, value) pair in the metadata table of the database
storeException(HttpServletRequest, String, ActionMessage, ActionForward, String) - Method in class org.intermine.web.struts.InterMineExceptionHandler
Default implementation for handling an ActionMessage generated from an Exception during Action delegation.
storeFinalSnps() - Method in class org.intermine.bio.dataconversion.EnsemblSnpDbConverter
Store the consequences as reference list to a SNP
storeInvites(Profile) - Method in class org.intermine.api.bag.InvitationHandler
 
storeItems() - Method in class org.intermine.bio.dataconversion.OboConverter
Convert DagTerms into Items and relation Items, and write them to the ItemWriter
storeLargeBinary(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager
Returns an OutputStream object with which to write a large binary value to the database.
StoreMetadataTask - Class in org.intermine.task
Store model metadata to a database
StoreMetadataTask() - Constructor for class org.intermine.task.StoreMetadataTask
 
storeSavedBag() - Method in class org.intermine.api.profile.StorableBag
Perform the actual insertion of data into the userprofile database.
storeTrack(Track) - Method in class org.intermine.api.tracker.AbstractTracker
Save into the table the track object representing the user activity
storeTrack(Track) - Method in interface org.intermine.api.tracker.Tracker
Save into the table a Track
storeWithConnection(Connection, Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Performs store with a given Connection.
StreamedOutput - Class in org.intermine.webservice.server.output
Immediately as the data or error messages are added they are streamed via http connection.
StreamedOutput(PrintWriter, Formatter) - Constructor for class org.intermine.webservice.server.output.StreamedOutput
Constructor.
StreamedOutput(PrintWriter, Formatter, String) - Constructor for class org.intermine.webservice.server.output.StreamedOutput
Constructor.
STRICT_NOT_EQUALS - Static variable in class org.intermine.metadata.ConstraintOp
Require that the two arguments are not equal
STRING_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint
 
StringConstructor - Class in org.intermine.model
A CharSequence object representing a String constructed out of a sequence of other Strings.
StringConstructor() - Constructor for class org.intermine.model.StringConstructor
Main constructor - creates an empty object.
StringHelper - Class in org.intermine.api.query.range
 
StringHelper() - Constructor for class org.intermine.api.query.range.StringHelper
 
StringTableExporter - Class in org.intermine.web.logic.export.string
Simple exporter exporting table of strings.
StringTableExporter(PrintWriter, RowFormatter) - Constructor for class org.intermine.web.logic.export.string.StringTableExporter
Constructor.
stringToObject(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns an object for a given String.
stringToSource(String) - Method in class org.intermine.dataloader.DataTracker
Converts a string sourcename to a Source.
stringToSource(String, String) - Method in class org.intermine.dataloader.DataTracker
Converts a string sourcename to a Source if the type is known.
StringUtil - Class in org.intermine.metadata
Collection of commonly used String utilities
StringUtil.LineWrappedString - Class in org.intermine.metadata
Class for returning multiple values from the wrapLines method.
StringUtil.LineWrappedString(String, boolean) - Constructor for class org.intermine.metadata.StringUtil.LineWrappedString
Constructor.
stripStart(String, Properties) - Static method in class org.intermine.metadata.Util
Strips the given string off the keys of the given Properties, and returns a new set of properties.
stripStart(String, Properties) - Static method in class org.intermine.util.PropertiesUtil
Strips the given string off the keys of the given Properties, and returns a new set of properties.
STRPOS - Static variable in class org.intermine.sql.query.Function
STRPOS operator - takes two operands.
SUB - Static variable in class org.intermine.web.logic.config.HeaderConfigTitle
A subtitle.
SUBCLASSES - Static variable in class org.intermine.web.logic.Constants
ServletContext attribute, Map from unqualified type name to list of subclass names.
subclassValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
subIter - Variable in class org.intermine.api.results.ExportResultsIterator
 
subList(int, int) - Method in class org.intermine.objectstore.query.Results
subList(int, int) - Method in class org.intermine.webservice.client.results.ResultRowList
 
subMap - Variable in class org.intermine.util.ReferenceMap
 
SubMenuController - Class in org.intermine.web.struts
Controller for the submenu at the top of every page
SubMenuController() - Constructor for class org.intermine.web.struts.SubMenuController
 
submit(BagQueryRunner, JobInput) - Method in class org.intermine.api.idresolution.IDResolver
 
submit(BagQueryUpgrade) - Method in class org.intermine.api.idresolution.IDResolver
 
subquery - Variable in class org.intermine.objectstore.query.SubqueryConstraint
 
subquery - Variable in class org.intermine.objectstore.query.SubqueryExistsConstraint
 
SubQuery - Class in org.intermine.sql.query
A representation of a subquery that can be present in the FROM section of an SQL query.
SubQuery(Query, String) - Constructor for class org.intermine.sql.query.SubQuery
Constructor for this SubQuery object.
SubqueryConstraint - Class in org.intermine.objectstore.query
Constrain a QueryClass or QueryEvaluable to be within the select list of a given subquery.
SubqueryConstraint(QueryEvaluable, ConstraintOp, Query) - Constructor for class org.intermine.objectstore.query.SubqueryConstraint
Construct a SubqueryConstraint with a QueryEvaluable
SubqueryConstraint(QueryClass, ConstraintOp, Query) - Constructor for class org.intermine.objectstore.query.SubqueryConstraint
Construct a SubqueryConstraint with a QueryClass
SubQueryConstraint - Class in org.intermine.sql.query
A representation of a constraint where an AbstractValue is IN the results of a Query.
SubQueryConstraint(AbstractValue, Query) - Constructor for class org.intermine.sql.query.SubQueryConstraint
Constructor for SubQueryConstraint object.
subqueryConstraintToString(SqlGenerator.State, StringBuffer, SubqueryConstraint, Query, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a SubqueryConstraint object into a String suitable for putting in an SQL query.
SubqueryExistsConstraint - Class in org.intermine.objectstore.query
Check if there are any rows in the subquery
SubqueryExistsConstraint(ConstraintOp, Query) - Constructor for class org.intermine.objectstore.query.SubqueryExistsConstraint
Construct a SubqueryExistsConstraint
subqueryExistsConstraintToString(SqlGenerator.State, StringBuffer, SubqueryExistsConstraint, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a SubqueryExistsConstraint object into a String suitable for putting in an SQL query.
subscribe(String, Properties) - Static method in class org.intermine.util.MailUtils
Subscribe the given email address to the mailing list specified in the mine config file
subscribeToList(String) - Method in class org.intermine.util.Emailer
Subscribe a user to a mailing list.
subscribeToList(String) - Method in class org.intermine.web.context.NullMailer
 
subsegment(int, int) - Method in class org.intermine.webservice.server.jbrowse.Segment
 
subSequence(int, int) - Method in class org.intermine.bio.util.ClobAccessReverseComplement
Returns a new CharSequence that is a subsequence of this sequence, from start (inclusive) to end (exclusive).
subSequence(int, int) - Method in class org.intermine.model.StringConstructor
subSequence - Variable in class org.intermine.objectstore.query.ClobAccess
 
subSequence(int, int) - Method in class org.intermine.objectstore.query.ClobAccess
Returns a new CharSequence that is a subsequence of this sequence, from start (inclusive) to end (exclusive).
subSequence(int, int) - Method in class org.intermine.objectstore.query.PendingClob
Returns a new CharSequence that is a subsequence of this sequence, from start (inclusive) to end (exclusive).
SUBSTR - Static variable in class org.intermine.sql.query.Function
SUBSTR operator - takes two or three operands.
SUBSTRING - Static variable in class org.intermine.objectstore.query.QueryExpression
Substring of specified length from index in string
SubTable - Class in org.intermine.webservice.server.core
A class that represents a table nested within a cell in another table.
SubTable(Path, List<Path>, List<List<Either<ResultCell, SubTable>>>) - Constructor for class org.intermine.webservice.server.core.SubTable
Construct a sub table.
subtabs - Variable in class org.intermine.web.logic.results.WebState
 
SUBTRACT - Static variable in class org.intermine.api.bag.BagOperations
Constant representing logical substraction.
subtract(Model, Collection<InterMineBag>, String, Profile, ClassKeys) - Static method in class org.intermine.api.bag.BagOperations
Create a bag that contains the union of the bags provided minus the intersection of those bags.
SUBTRACT - Static variable in class org.intermine.objectstore.query.QueryExpression
Subtraction of two numeric fields
subtract(ItemList...) - Method in class org.intermine.webservice.client.lists.ItemList
Remove the items in the given lists from this list.
subtract(ListService.ListOperationInfo, ItemList...) - Method in class org.intermine.webservice.client.lists.ItemList
Remove the items in the given lists from this list.
subtract(Collection<ItemList>) - Method in class org.intermine.webservice.client.lists.ItemList
Remove the items in the given lists from this list.
subtract(ListService.ListOperationInfo, Collection<ItemList>) - Method in class org.intermine.webservice.client.lists.ItemList
Remove the items in the given lists from this list.
subtract(ListService.ListOperationInfo, ItemList, ItemList...) - Method in class org.intermine.webservice.client.services.ListService
Subtract some lists from some other lists to produce a new list.
subtract(ListService.ListOperationInfo, ItemList[], ItemList...) - Method in class org.intermine.webservice.client.services.ListService
Subtract some lists from some other lists to produce a new list.
subtract(ItemList, ItemList...) - Method in class org.intermine.webservice.client.services.ListService
Subtract some lists from some other lists to produce a new list.
subtract(ItemList[], ItemList...) - Method in class org.intermine.webservice.client.services.ListService
Subtract some lists from some other lists to produce a new list.
subtract(Collection<ItemList>, Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService
Subtract some lists from some other lists to produce a new list.
subtract(ListService.ListOperationInfo, Collection<ItemList>, Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService
Subtract some lists from some other lists to produce a new list.
SUBTRACT_PARAM - Static variable in class org.intermine.webservice.server.lists.ListInput
Things to subtract
SUFFIX - Static variable in class org.intermine.bio.webservice.GenomicRegionBedService
 
SUFFIX - Static variable in class org.intermine.bio.webservice.GenomicRegionFastaService
 
SUM - Static variable in class org.intermine.objectstore.query.QueryFunction
Sum of a number of rows
SUM - Static variable in class org.intermine.sql.query.Function
SUM(v) aggregate function - takes one operand.
summarise(ApiTemplate) - Method in class org.intermine.api.template.TemplateSummariser
Populates the possibleValues data for a given TemplateQuery from the os.
summarise(String) - Method in class org.intermine.dwr.AjaxServices
Summarises the given template query.
summariseAsOccurrences(String) - Static method in class org.intermine.api.query.MainHelper.SummaryConfig
Returns whether the given field name is configured to be summarised as a count of occurrences.
SummariseObjectStoreTask - Class in org.intermine.task
Summarise an ObjectStore into a particular properties file.
SummariseObjectStoreTask() - Constructor for class org.intermine.task.SummariseObjectStoreTask
 
summariseQuery(PathQuery, String, boolean) - Method in class org.intermine.api.query.QueryExecutor
Returns the results for a summary for a column in a PathQuery.
summariseQuery(PathQuery, String) - Method in class org.intermine.api.query.QueryExecutor
 
summariseQuery(PathQuery, String, String, boolean) - Method in class org.intermine.api.query.QueryExecutor
Summarise a query.
SummariseTemplatesAction - Class in org.intermine.web.struts
Action to summarise all templates.
SummariseTemplatesAction() - Constructor for class org.intermine.web.struts.SummariseTemplatesAction
 
summaryBatchSize - Variable in class org.intermine.api.query.QueryExecutor
 
summaryCallCounts - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher
 
SummaryConstraint - Class in org.intermine.web.logic.querybuilder
Representation of a PathQuery constraint with additional information for display in the QueryBuilder summary section.
SummaryConstraint(PathConstraint, String, boolean, String, String) - Constructor for class org.intermine.web.logic.querybuilder.SummaryConstraint
Construct with the underlying PathConstraint and additional details from the PathQuery.
summaryCounts - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher
 
SummaryPath - Class in org.intermine.web.logic.querybuilder
Representation of a query path with additional information for display in the QueryBulder summary section.
SummaryPath(Path, boolean, boolean) - Constructor for class org.intermine.web.logic.querybuilder.SummaryPath
Construct a summary path with details of whether the path is locked and/or forced to be an inner join.
SummaryService - Class in org.intermine.webservice.server
Serve up the paths used to summarise each class.
SummaryService(InterMineAPI) - Constructor for class org.intermine.webservice.server.SummaryService
Constructor
SummaryServlet - Class in org.intermine.webservice.server
Returns a summary field information.
SummaryServlet() - Constructor for class org.intermine.webservice.server.SummaryServlet
 
summaryTimes - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher
 
superUsers - Variable in class org.intermine.web.struts.ModifySuperUserForm
 
swapColumns(int, int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Swap 2 columns
swapColumns(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction
Deprecated.
as we don't move columns any more
switchable - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
SwitchOffAbility - Enum in org.intermine.template
Enumeration for describing the configuration on constraints on a TemplateQuery that determines whether a user is allowed to switch off a constraint, and if so what state it is in.
symbol - Variable in class org.intermine.bio.dataconversion.TreefamConverter.GeneHolder
 
SymmetricDifference - Class in org.intermine.api.bag.operations
 
SymmetricDifference(Model, Profile, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.SymmetricDifference
 
SynchronisedIterator<E> - Class in org.intermine.util
An Iterator that passes through to an underlying Iterator, synchronising all calls.
SynchronisedIterator(Iterator<E>) - Constructor for class org.intermine.util.SynchronisedIterator
Constructs a SynchronisedIterator from an Iterator.
synchroniseWithDatabase(Connection) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Synchronise with the underlying database
synonyms - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord
 
synonyms - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler
 
synToItem - Variable in class org.intermine.bio.dataconversion.OboConverter
 

T

TabFormatter - Class in org.intermine.webservice.server.output
Formats data to tab separated data format.
TabFormatter() - Constructor for class org.intermine.webservice.server.output.TabFormatter
Constructor.
TabFormatter(boolean) - Constructor for class org.intermine.webservice.server.output.TabFormatter
Construct, specifying whether or not to quote.
TabHttpExporter - Class in org.intermine.web.logic.export.http
Exporter that exports table with results in tab format.
TabHttpExporter() - Constructor for class org.intermine.web.logic.export.http.TabHttpExporter
Constructor.
table - Variable in class org.intermine.sql.logging.DatabaseWriter
 
table - Variable in class org.intermine.sql.query.Field
 
Table - Class in org.intermine.sql.query
A representation of a table that can be present in the FROM section of an SQL query.
Table(String, String) - Constructor for class org.intermine.sql.query.Table
Constructor for this Table object.
Table(String) - Constructor for class org.intermine.sql.query.Table
Constructor for this Table object, without an alias.
Table - Interface in org.intermine.sql.writebatch
An interface representing all changes to be made to an SQL table of some sort.
TABLE_INDEX - Static variable in class org.intermine.sql.precompute.PrecomputedTableManager
 
TABLE_MAP - Static variable in class org.intermine.web.logic.Constants
Session attribute that holds cache of table identifiers to PagedTable objects.
TABLE_NAME - Static variable in class org.intermine.api.bag.SharingInvite
The DB table that holds the invitations
TableBatch - Class in org.intermine.sql.writebatch
A class representing all changes to be made to an SQL table.
TableBatch() - Constructor for class org.intermine.sql.writebatch.TableBatch
Constructor for this class.
TableCell - Class in org.intermine.webservice.server.core
A representation of a table cell.
TableCell(FastPathObject, Path, boolean) - Constructor for class org.intermine.webservice.server.core.TableCell
Construct a table cell.
TableCell(Path) - Constructor for class org.intermine.webservice.server.core.TableCell
Construct a table cell for a null value.
TableCellFormatter - Class in org.intermine.webservice.server.output
A formatter that will render a table cell.
TableCellFormatter(InterMineAPI) - Constructor for class org.intermine.webservice.server.output.TableCellFormatter
 
TableController - Class in org.intermine.web.struts
Implementation of TilesAction.
TableController() - Constructor for class org.intermine.web.struts.TableController
 
tableCount - Variable in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
 
tableExists(Connection, String) - Static method in class org.intermine.sql.DatabaseUtil
Tests if a table exists in the database
TableExportAction - Class in org.intermine.web.struts
Implementation of Action that allows the user to export a PagedTable to a file.
TableExportAction() - Constructor for class org.intermine.web.struts.TableExportAction
 
TableExportConfig - Class in org.intermine.web.logic.config
Configuration information for exporting.
TableExportConfig() - Constructor for class org.intermine.web.logic.config.TableExportConfig
 
TableExporterFactory - Class in org.intermine.web.logic.export.http
Factory class that creates and registers TableHttpExporter classes.
TableExporterFactory(WebConfig) - Constructor for class org.intermine.web.logic.export.http.TableExporterFactory
Constructor.
TableExportForm - Class in org.intermine.web.struts
Form to hold options for exporting.
TableExportForm() - Constructor for class org.intermine.web.struts.TableExportForm
Constructor
TableHttpExporter - Interface in org.intermine.web.logic.export.http
Implemented by objects that can export PagedTable.
TableJSONProcessor - Class in org.intermine.webservice.server.widget
Class to process the result returned by a table widgets in JSON format
TableJSONProcessor() - Constructor for class org.intermine.webservice.server.widget.TableJSONProcessor
 
tableNameForId(Class<?>, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Returns the table name used by the ID fetch query.
tablenamesCache - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
 
TableRowIterator - Class in org.intermine.webservice.server.core
A class for iterating over rows of results returned from the object store in a way that is very similar in shape to the raw results, but more tractable and more easily serialised and handled in other places.
TableRowIterator(PathQuery, Query, Results, Map<String, QuerySelectable>, Page, InterMineAPI) - Constructor for class org.intermine.webservice.server.core.TableRowIterator
Constructor.
TableRowService - Class in org.intermine.webservice.server.query.result
A service that produces results in nested rows for use in tables.
TableRowService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.result.TableRowService
 
tablesAltered - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
TableTag - Class in org.intermine.web.tags.table
Class rendering html table.
TableTag() - Constructor for class org.intermine.web.tags.table.TableTag
 
tableToCollections - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
tableToColNameArray - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
tableToInfo - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
TableWidget - Class in org.intermine.web.logic.widget
A table widget gets the values for a given path for all the items in a list.
TableWidget(TableWidgetConfig, InterMineBag, ObjectStore) - Constructor for class org.intermine.web.logic.widget.TableWidget
 
TableWidgetConfig - Class in org.intermine.web.logic.widget.config
 
TableWidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.TableWidgetConfig
 
TableWidgetLdr - Class in org.intermine.web.logic.widget
 
TableWidgetLdr(WidgetConfig, InterMineBag, ObjectStore) - Constructor for class org.intermine.web.logic.widget.TableWidgetLdr
This class loads and formats the data for the count table widgets in the bag details page
TableWidgetService - Class in org.intermine.webservice.server.widget
Web service that returns a table widget for a given list.
TableWidgetService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.TableWidgetService
Construct a TableWidgetService
TableWidgetsServlet - Class in org.intermine.webservice.server.widget
Servlet running WidgetsService.
TableWidgetsServlet() - Constructor for class org.intermine.webservice.server.widget.TableWidgetsServlet
 
TableXMLProcessor - Class in org.intermine.webservice.server.widget
Class to process the result returned by a table widgets into a XML format
TabRowFormatter - Class in org.intermine.web.logic.export.rowformatters
Row formatter formats line as tab separated strings.
TabRowFormatter() - Constructor for class org.intermine.web.logic.export.rowformatters.TabRowFormatter
Constructor.
TabTableResult - Class in org.intermine.webservice.client.results
A utility class for parsing tab separated values in the results.
TabTableResult(HttpConnection) - Constructor for class org.intermine.webservice.client.results.TabTableResult
Constructor.
TabTableResult(String) - Constructor for class org.intermine.webservice.client.results.TabTableResult
Constructor.
TagBinding - Class in org.intermine.api.xml
Convert Tags from the Profile to and from XML
TagBinding() - Constructor for class org.intermine.api.xml.TagBinding
 
TagChecker - Interface in org.intermine.api.profile
An interface for checking the validity of tags.
TagFilter - Class in org.intermine.api.search
Class for filtering web-searchables based on their tags.
TagFilter(Collection<String>, Profile, String) - Constructor for class org.intermine.api.search.TagFilter
Constructor
Taggable - Interface in org.intermine.api.profile
An interface for items that may have tags stored for them in the user profile database.
TaggingEvent - Class in org.intermine.api.search
A representation of a notification that a tag has been changed on a web-searchable item.
TaggingEvent(WebSearchable, String, TaggingEvent.TagChange) - Constructor for class org.intermine.api.search.TaggingEvent
Constructor.
TaggingEvent.TagChange - Enum in org.intermine.api.search
The possible actions that this event can represent.
TagHandler - Class in org.intermine.api.profile
Extension of PathQueryHandler to handle parsing TemplateQueries
TagHandler(String, Set) - Constructor for class org.intermine.api.profile.TagHandler
Constructor
TagHandler(ProfileManager, String) - Constructor for class org.intermine.api.profile.TagHandler
Constructor
TagManager - Class in org.intermine.api.profile
Manager class for tags.
TagManager(ObjectStoreWriter) - Constructor for class org.intermine.api.profile.TagManager
Constructor.
tagManager - Variable in class org.intermine.api.search.SearchRepository
 
TagManager.TagException - Exception in org.intermine.api.profile
Class for reporting exceptions from tag manipulation actions.
TagManager.TagException(String) - Constructor for exception org.intermine.api.profile.TagManager.TagException
Constructor.
TagManager.TagNameException - Exception in org.intermine.api.profile
Class for representing errors due to the use of illegal tag names.
TagManager.TagNameException() - Constructor for exception org.intermine.api.profile.TagManager.TagNameException
Constructor.
TagManager.TagNamePermissionException - Exception in org.intermine.api.profile
Class for representing errors due to the restricted nature of some tags.
TagManager.TagNamePermissionException() - Constructor for exception org.intermine.api.profile.TagManager.TagNamePermissionException
Constructor.
TagManager.TagNamePermissionException(String) - Constructor for exception org.intermine.api.profile.TagManager.TagNamePermissionException
Constructor.
TagManagerFactory - Class in org.intermine.api.profile
Factory class for creating TagManager objects.
TagManagerFactory(ObjectStoreWriter) - Constructor for class org.intermine.api.profile.TagManagerFactory
Constructor.
TagManagerFactory(ProfileManager) - Constructor for class org.intermine.api.profile.TagManagerFactory
Constructor.
TagMapper - Class in org.intermine.api.profile
A class that handles transforming a list of tags into a list of strings of different types.
TagMapper.Field - Enum in org.intermine.api.profile
The valid fields that can be read from a tag
tagName - Variable in class org.intermine.api.search.TaggingEvent
 
TagNames - Class in org.intermine.api.tag
 
TAGS_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
Tags to apply
TagTypes - Class in org.intermine.api.tag
Known tag types.
targetAlias - Variable in class org.intermine.bio.task.GFF3ConverterTask
 
taxon - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord
 
taxonId - Variable in class org.intermine.bio.dataconversion.HomologeneConverter.GeneRecord
 
taxonId - Variable in class org.intermine.bio.dataconversion.TreefamConverter.GeneHolder
 
TEMP_SUFFIX - Static variable in class org.intermine.webservice.server.lists.ListInput
A suffix to attach to temporary lists
tempDir - Variable in class org.intermine.task.BuildDbTask
 
TEMPLATE - Static variable in class org.intermine.api.tag.TagTypes
Template.
TEMPLATE_ACTION_PATH - Static variable in class org.intermine.web.struts.TemplateAction
path of TemplateAction action
TEMPLATE_BAG_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
TEMPLATE_BAG_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
 
TEMPLATE_BAG_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
TEMPLATE_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of class that tracks templates
TEMPLATE_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of table that tracks templates
TemplateAction - Class in org.intermine.web.struts
Action to handle submit from the template page.
TemplateAction() - Constructor for class org.intermine.web.struts.TemplateAction
 
templateButton - Variable in class org.intermine.web.struts.ModifyTemplateForm
 
TemplateComparator - Class in org.intermine.template
Comparator used for ordering templates by title
TemplateComparator() - Constructor for class org.intermine.template.TemplateComparator
 
TemplateController - Class in org.intermine.web.struts
Controller for the template tile.
TemplateController() - Constructor for class org.intermine.web.struts.TemplateController
 
templateExecutions - Variable in class org.intermine.api.tracker.TemplatesExecutionMap
 
TemplateForm - Class in org.intermine.web.struts
Form to handle input from the template page
TemplateForm() - Constructor for class org.intermine.web.struts.TemplateForm
Constructor
templateFormToTemplateValues(TemplateForm, TemplateQuery) - Method in class org.intermine.web.struts.TemplateAction
The method returns a map of TemplateValue for each editable constraint.
TemplateHelper - Class in org.intermine.api.template
Static helper routines related to templates.
templateIsPublic(TemplateQuery, InterMineAPI, Profile) - Static method in class org.intermine.web.struts.WebserviceCodeGenAction
Utility function to determine whether the template is publicly accessible.
templateLabel - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
TemplateListAppendService - Class in org.intermine.webservice.server.template
A class to append items from a set of template results to a list.
TemplateListAppendService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.TemplateListAppendService
Constructor.
TemplateListAppendServlet - Class in org.intermine.webservice.server.template
Runs the query-to-list service to run queries and save them as lists.
TemplateListAppendServlet() - Constructor for class org.intermine.webservice.server.template.TemplateListAppendServlet
 
TemplateListController - Class in org.intermine.web.struts
Controller for the template list tile.
TemplateListController() - Constructor for class org.intermine.web.struts.TemplateListController
 
templateManager - Variable in class org.intermine.api.InterMineAPI
 
TemplateManager - Class in org.intermine.api.template
A TemplateManager provides access to all global and/or user templates and methods to fetch them by type, etc.
TemplateManager(Profile, Model) - Constructor for class org.intermine.api.template.TemplateManager
The TemplateManager references the super user profile to fetch global templates.
TemplateManager(Profile, Model, TemplateTracker) - Constructor for class org.intermine.api.template.TemplateManager
The TemplateManager references the super user profile to fetch global templates.
templateMapToXml(Map<String, TemplateQuery>, int) - Static method in class org.intermine.api.template.TemplateHelper
Given a Map of TemplateQueries (mapping from template name to TemplateQuery) return a string containing each template seriaised as XML.
TemplateParameter - Class in org.intermine.webservice.client.template
A simple class representing the group of parameters that define a template constraint A template parameter is a predefined constraint where you can specify the constraint operation and the constrained value.
TemplateParameter(String, String, String, String, String) - Constructor for class org.intermine.webservice.client.template.TemplateParameter
Create a new TemplateParameter for a simple value constraint.
TemplateParameter(String, String, Collection<String>, String) - Constructor for class org.intermine.webservice.client.template.TemplateParameter
Create a new TemplateParameter for a multi-value constraint.
TemplateParameter(String, String, String, String) - Constructor for class org.intermine.webservice.client.template.TemplateParameter
Create a new TemplateParameter for a unary constraint (such as IS NULL).
TemplatePopulator - Class in org.intermine.api.template
Configures original template.
TemplatePopulatorException - Exception in org.intermine.template
Exception thrown when errors occur populating a template query with values.
TemplatePopulatorException(String) - Constructor for exception org.intermine.template.TemplatePopulatorException
Constructs an TemplatePopulatorException with the specified detail message.
TemplatePopulatorException(Throwable) - Constructor for exception org.intermine.template.TemplatePopulatorException
Constructs an TemplatePopulatorException with the specified nested throwable.
TemplatePopulatorException(String, Throwable) - Constructor for exception org.intermine.template.TemplatePopulatorException
Constructs an TemplatePopulatorException with the specified detail message and nested throwable.
TemplatePrecomputeHelper - Class in org.intermine.api.template
Helper class providing methods for precomputing and summarising TemplateQuery objects.
TemplateProblemsController - Class in org.intermine.web.struts
Called before templateProblems.jsp
TemplateProblemsController() - Constructor for class org.intermine.web.struts.TemplateProblemsController
 
TemplateQuery - Class in org.intermine.template
A template query, which consists of a PathQuery, description, category, short name.
TemplateQuery(String, String, String, PathQuery) - Constructor for class org.intermine.template.TemplateQuery
Construct a new instance of TemplateQuery.
TemplateQuery(TemplateQuery) - Constructor for class org.intermine.template.TemplateQuery
Copy constructor.
TemplateQueryBinding - Class in org.intermine.template.xml
Convert PathQueries to and from XML
TemplateQueryBinding() - Constructor for class org.intermine.template.xml.TemplateQueryBinding
 
TemplateQueryHandler - Class in org.intermine.template.xml
Extension of PathQueryHandler to handle parsing TemplateQueries
TemplateQueryHandler(Map<String, TemplateQuery>, int) - Constructor for class org.intermine.template.xml.TemplateQueryHandler
Constructor
TemplateQueryUpdate - Class in org.intermine.api.profile
A class to update template queries to match a new Data model.
TemplateQueryUpdate(ApiTemplate, Model) - Constructor for class org.intermine.api.profile.TemplateQueryUpdate
Constructor.
TemplateRemovalService - Class in org.intermine.webservice.server.template
A service that deletes templates.
TemplateRemovalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.TemplateRemovalService
 
TemplateResultInput - Class in org.intermine.web.logic.template
TemplateResultInput is parameter object representing parameters for TemplateResultService web service.
TemplateResultInput() - Constructor for class org.intermine.web.logic.template.TemplateResultInput
 
TemplateResultLinkGenerator - Class in org.intermine.webservice.server.template.result
Class that implements generating links of TemplateResultService web service.
TemplateResultLinkGenerator() - Constructor for class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
 
TemplateResultRequestParser - Class in org.intermine.webservice.server.template.result
Processes service request.
TemplateResultRequestParser(HttpServletRequest) - Constructor for class org.intermine.webservice.server.template.result.TemplateResultRequestParser
TemplateResultRequestProcessor constructor.
TemplateResultService - Class in org.intermine.webservice.server.template.result
Web service that returns results of public template constrained with values in request.
TemplateResultService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.result.TemplateResultService
Construct with an InterMineAPI.
TemplateResultServlet - Class in org.intermine.webservice.server.template.result
Runs TemplateResultService web service.
TemplateResultServlet() - Constructor for class org.intermine.webservice.server.template.result.TemplateResultServlet
 
Templates - Class in org.intermine.web.logic.template
A utility class with static methods for dealing with templates.
Templates.TemplateValueParseException - Exception in org.intermine.web.logic.template
An exception that we throw when we can't parse a template.
Templates.TemplateValueParseException(String) - Constructor for exception org.intermine.web.logic.template.Templates.TemplateValueParseException
Construct an exception with a message
TEMPLATES_PARAMETER - Static variable in class org.intermine.webservice.server.template.TemplateUploadService
The key for the templates parameter
TemplatesController - Class in org.intermine.web.struts
Tiles controller for templates tile (page).
TemplatesController() - Constructor for class org.intermine.web.struts.TemplatesController
 
TemplateService - Class in org.intermine.webservice.client.services
The TemplateService represents the connection to the resource that returns results of templates and number of results.
TemplateService(String, String) - Constructor for class org.intermine.webservice.client.services.TemplateService
Use ServiceFactory instead of constructor for creating this service.
TemplateService.TemplateRequest - Class in org.intermine.webservice.client.services
A subclass of RequestImpl relevant to template queries.
TemplateService.TemplateRequest(Request.RequestType, String, ContentType) - Constructor for class org.intermine.webservice.client.services.TemplateService.TemplateRequest
Constructor.
TemplateSettingsForm - Class in org.intermine.web.struts
Form used when building a template.
TemplateSettingsForm() - Constructor for class org.intermine.web.struts.TemplateSettingsForm
 
TemplatesExecutionMap - Class in org.intermine.api.tracker
Class for saving the template executions into the memory.
TemplatesExecutionMap() - Constructor for class org.intermine.api.tracker.TemplatesExecutionMap
 
TemplatesExportAction - Class in org.intermine.web.struts
Exports templates to XML.
TemplatesExportAction() - Constructor for class org.intermine.web.struts.TemplatesExportAction
 
TemplatesImportAction - Class in org.intermine.web.struts
Imports templates in XML format.
TemplatesImportAction() - Constructor for class org.intermine.web.struts.TemplatesImportAction
 
TemplatesImportForm - Class in org.intermine.web.struts
Form bean representing template import form.
TemplatesImportForm() - Constructor for class org.intermine.web.struts.TemplatesImportForm
 
templateSummariser - Variable in class org.intermine.api.InterMineAPI
 
TemplateSummariser - Class in org.intermine.api.template
This class manages summaries of possible values for editable constraints for template queries.
TemplateSummariser(ObjectStore, ObjectStoreWriter, ObjectStoreSummary) - Constructor for class org.intermine.api.template.TemplateSummariser
Construct a TemplateSummariser.
TemplateToListService - Class in org.intermine.webservice.server.template
A service for turning the results of a template query into a list.
TemplateToListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.TemplateToListService
Constructor
TemplateToListServlet - Class in org.intermine.webservice.server.template
Runs the template-to-list service to run templates and save them as lists.
TemplateToListServlet() - Constructor for class org.intermine.webservice.server.template.TemplateToListServlet
 
TemplateTrack - Class in org.intermine.api.tracker.track
Class to represent the track for the templates objects.
TemplateTrack(String, String, String, Timestamp) - Constructor for class org.intermine.api.tracker.track.TemplateTrack
Create a template track
TemplateTrack(String, String, String) - Constructor for class org.intermine.api.tracker.track.TemplateTrack
Create a template track
TEMPLATETRACK - Static variable in class org.intermine.api.tracker.xml.TemplateTrackBinding
label for XML
TemplateTrackBinding - Class in org.intermine.api.tracker.xml
Code for reading and writing template tracks as XML.
TemplateTracker - Class in org.intermine.api.tracker
Class for tracking the templates execution by the users.
TemplateTracker(Queue<Track>) - Constructor for class org.intermine.api.tracker.TemplateTracker
 
TemplateTrackReadTask - Class in org.intermine.web.task
Task to read an templatetrack XML file of a webapp and saved into the userprofile database.
TemplateTrackReadTask() - Constructor for class org.intermine.web.task.TemplateTrackReadTask
 
TEMPLATETRACKS - Static variable in class org.intermine.api.tracker.xml.TemplateTrackBinding
label for XML
TemplateTrackWriteTask - Class in org.intermine.web.task
Task to write an XML file of template track contained in the user profile database.
TemplateTrackWriteTask() - Constructor for class org.intermine.web.task.TemplateTrackWriteTask
 
TemplateUploadService - Class in org.intermine.webservice.server.template
A service to enable templates to be uploaded.
TemplateUploadService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.TemplateUploadService
Constructor.
TemplateUploadServlet - Class in org.intermine.webservice.server.template
Runs the Template Upload Service to handle user template uploads.
TemplateUploadServlet() - Constructor for class org.intermine.webservice.server.template.TemplateUploadServlet
 
TemplateValue - Class in org.intermine.template
A TemplateValue represents the value for an editable constraint of a template query and details about what is being constrained.
TemplateValue(PathConstraint, ConstraintOp, TemplateValue.ValueType, SwitchOffAbility) - Constructor for class org.intermine.template.TemplateValue
Constructor.Construct with details of what we are constraining, but without the value.
TemplateValue(PathConstraint, ConstraintOp, String, TemplateValue.ValueType, SwitchOffAbility) - Constructor for class org.intermine.template.TemplateValue
Construct with the details of what we are constraining and the value.
TemplateValue(PathConstraint, ConstraintOp, String, TemplateValue.ValueType, String, SwitchOffAbility) - Constructor for class org.intermine.template.TemplateValue
Construct with the details of what we are constraining and the value.
TemplateValue(PathConstraint, ConstraintOp, TemplateValue.ValueType, List<String>, SwitchOffAbility) - Constructor for class org.intermine.template.TemplateValue
Construct with the details of what we are constraining and values.
TemplateValue.ValueType - Enum in org.intermine.template
Possible values for TemplateValue type.
TEN - Static variable in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
 
TEN_THOUSAND - Static variable in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
 
termClass - Variable in class org.intermine.bio.dataconversion.OboConverter
 
termClassName - Variable in class org.intermine.bio.dataconversion.GoConverter
 
termCollectionName - Variable in class org.intermine.bio.dataconversion.GoConverter
 
terms - Variable in class org.intermine.bio.ontology.OboParser
All terms.
terseClass(String) - Static method in class org.intermine.metadata.ClassDescriptor
Strips everything before the last dot out of a String.
TEST_STRING - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
TEXT_COUNT - Static variable in class org.intermine.webservice.client.core.ContentType
A ContentType constant that describes the generic text/plain content type when requesting counts.
TEXT_PLAIN - Static variable in class org.intermine.webservice.client.core.ContentType
A ContentType constant that describes the generic text/plain content type.
TEXT_TAB - Static variable in class org.intermine.webservice.client.core.ContentType
A ContentType constant that describes the generic text/plain content type.
TEXT_XML - Static variable in class org.intermine.webservice.client.core.ContentType
A ContentType constant that describes the generic text/xml content type.
TextTable - Class in org.intermine.metadata
A utility class for generating multi-column aligned text tables.
TextTable(boolean, boolean, boolean) - Constructor for class org.intermine.metadata.TextTable
Creates a new TextTable object, with or without column separating lines.
TextUtil - Class in org.intermine.api.util
 
tgtDir - Variable in class org.intermine.bio.dataconversion.UniprotFilterTask
 
tgtSequence - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler
 
then(Function<T, R>) - Method in class org.intermine.webservice.server.core.EitherVisitor
Compose this visitor with a function which consumes the output of this visitor.
THOUSAND - Static variable in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
 
THREAD_COUNT - Static variable in class org.intermine.task.PrecomputeTask
 
throwBestQueryException(String) - Method in class org.intermine.sql.precompute.BestQueryExplainer
Throws an exception.
throwBestQueryException(String) - Method in class org.intermine.sql.precompute.BestQueryExplainerVerbose
Throws an exception.
tickle() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Tell this object to continue returning false from shouldCancelQuery.
tickleCount - Variable in class org.intermine.web.logic.query.QueryMonitorTimeout
number of tickles. used to determine how.
time - Variable in class org.intermine.dataconversion.FullXmlConverter
 
timeLimit - Variable in class org.intermine.sql.precompute.BestQueryExplainer
 
times - Variable in class org.intermine.dataconversion.FullXmlConverter
 
timeSpentExecute - Variable in class org.intermine.dataloader.BatchingFetcher
 
timeSpentPrefetchEquiv - Variable in class org.intermine.dataloader.BatchingFetcher
 
timeSpentPrefetchTracker - Variable in class org.intermine.dataloader.BatchingFetcher
 
timeSpentRecursing - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
timestamp - Variable in class org.intermine.api.tracker.track.TrackAbstract
 
toAdditionsXML() - Method in class org.intermine.metadata.Model
Used to generate the SO additions file
toArray() - Method in class org.intermine.util.PseudoSet
toArray(T[]) - Method in class org.intermine.util.PseudoSet
toArray() - Method in class org.intermine.webservice.client.results.ResultRowList
 
toArray(T[]) - Method in class org.intermine.webservice.client.results.ResultRowList
 
toBED() - Method in class org.intermine.bio.io.bed.BEDRecord
Return this record in BED format.
toBED() - Method in class org.intermine.bio.io.gaf.GAFRecord
Return this record in BED format.
toGFF3() - Method in class org.intermine.bio.io.gff3.GFF3Record
Return this record in GFF format.
toIntegers(Collection<String>) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Convert a set of Strings to a set of Integers using identifierToId()
toItems(Collection<FastPathObject>, Model) - Static method in class org.intermine.xml.full.FullRenderer
Convert a collection of Objects to Item format.
toJson() - Method in class org.intermine.pathquery.PathQuery
Convert this PathQuery to a JSON serialisation.
toJson(boolean) - Method in class org.intermine.pathquery.PathQuery
Convert this PathQuery to a JSON serialisation.
toJSON() - Method in class org.intermine.template.TemplateQuery
Returns a JSON string representation of the template query.
toJSON(ResultCell) - Method in class org.intermine.webservice.server.output.TableCellFormatter
Get the JSONObject that represents each cell in the results row
toJsonAST() - Method in class org.intermine.metadata.Model
Returns a data structure suitable for serialisation, eg. as JSON.
toJSONString() - Method in class org.intermine.metadata.AttributeDescriptor
Return the JSON representation of this object.
toJSONString() - Method in class org.intermine.metadata.ClassDescriptor
 
toJSONString() - Method in class org.intermine.metadata.FieldDescriptor
Return the JSON representation of this object.
toJSONString() - Method in class org.intermine.metadata.ReferenceDescriptor
Return the JSON representation of this object.
token - Variable in class org.intermine.web.struts.PasswordResetForm
 
tokenFactory - Variable in class org.intermine.webservice.server.user.NewDeletionTokenService
 
tokenHasMoreUses(String) - Method in class org.intermine.api.profile.ProfileManager
Return whether the token given in input is suitable for using in the future.
tokenise(String) - Method in class org.intermine.api.query.LookupTokeniser
Transform an input string into a list of identifiers.
tokenize(String, String) - Static method in class org.intermine.metadata.StringUtil
 
tokenize(String) - Static method in class org.intermine.metadata.StringUtil
Returns a list of tokens delimited by whitespace in String str (useful when handling XML)
tokenize(String, boolean) - Static method in class org.intermine.metadata.StringUtil
Returns a list of tokens delimited by comma.
tokenize(String) - Static method in class org.intermine.metadata.Util
Returns a list of tokens delimited by whitespace in String str (useful when handling XML)
TokenService - Class in org.intermine.webservice.server.user
A service that issues new tokens to a user.
TokenService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.TokenService
 
TokenServlet - Class in org.intermine.webservice.server.user
 
TokenServlet() - Constructor for class org.intermine.webservice.server.user.TokenServlet
 
TokensService - Class in org.intermine.webservice.server.user
Service that lets a user inspect their currently active tokens
TokensService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.TokensService
 
toMap() - Method in class org.intermine.bio.dataconversion.UniprotEntry.Dbref
 
toMap(ResultCell) - Method in class org.intermine.webservice.server.output.TableCellFormatter
 
toProperties() - Method in class org.intermine.objectstore.ObjectStoreSummary
Convert this summary to a properties object
toQuery() - Method in class org.intermine.objectstore.query.iql.IqlQuery
Convert to a InterMine query
toRangeString() - Method in class org.intermine.webservice.server.jbrowse.Segment
 
TorqueModelOutput - Class in org.intermine.objectstore.intermine
Map InterMine metadata to a Torque database schema in InterMine format
TorqueModelOutput(DatabaseSchema, File) - Constructor for class org.intermine.objectstore.intermine.TorqueModelOutput
Constructor for this class
TorqueModelOutputTask - Class in org.intermine.objectstore.intermine
Creates and runs a ModelOutput process to generate java or config files.
TorqueModelOutputTask() - Constructor for class org.intermine.objectstore.intermine.TorqueModelOutputTask
 
toSameInitialCase(String, String) - Static method in class org.intermine.metadata.StringUtil
Returns a string with the same initial letter case as the template string
toString() - Method in class org.intermine.api.bag.BagQuery
toString() - Method in class org.intermine.api.bag.SharingInvite
 
toString() - Method in class org.intermine.api.beans.ObjectDetails
 
toString() - Method in class org.intermine.api.beans.PartnerLink
 
toString() - Method in class org.intermine.api.idresolution.ResolutionJob
 
toString() - Method in class org.intermine.api.mines.ObjectRequest
 
toString() - Method in class org.intermine.api.profile.BagValue
 
toString() - Method in class org.intermine.api.profile.InterMineBag
 
toString() - Method in class org.intermine.api.results.Column
toString() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
toString() - Method in class org.intermine.api.results.flatouterjoins.MultiRowLaterValue
toString() - Method in class org.intermine.api.results.ResultElement
Returns a String representation of the ResultElement.
toString() - Method in class org.intermine.api.search.SearchResult
 
toString() - Method in class org.intermine.api.search.SearchTarget
 
toString() - Method in class org.intermine.bio.dataconversion.UniprotConverter.DiseaseHolder
 
toString() - Method in class org.intermine.bio.io.bed.BEDRecord
toString() - Method in class org.intermine.bio.io.gaf.GAFRecord
toString() - Method in class org.intermine.bio.io.gff3.GFF3Record
toString() - Method in class org.intermine.bio.ontology.OboTerm
Create a string representation of the term.
toString() - Method in class org.intermine.bio.ontology.OboTermSynonym
toString() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
 
toString() - Method in class org.intermine.bio.util.ClobAccessReverseComplement
Converts the Clob into a String.
toString() - Method in class org.intermine.bio.util.OrganismData
toString() - Method in class org.intermine.bio.web.model.GenomicRegion
 
toString() - Method in class org.intermine.dataconversion.MockItemWriter
toString() - Method in class org.intermine.dataloader.Source
toString() - Method in class org.intermine.metadata.AttributeDescriptor
toString() - Method in class org.intermine.metadata.ClassDescriptor
toString() - Method in class org.intermine.metadata.CollectionDescriptor
toString() - Method in class org.intermine.metadata.ConstraintOp
Get the String representation of this ConstraintOp
toString() - Method in class org.intermine.metadata.Model
toString() - Method in class org.intermine.metadata.PrimaryKey
toString() - Method in class org.intermine.metadata.ReferenceDescriptor
toString() - Method in class org.intermine.metadata.TextTable
Returns a text-formatted representation of this table.
toString() - Method in class org.intermine.model.StringConstructor
Returns the String that this object represents - note that this method should be avoided, because it defeats the purpose of keeping the constituent Strings separate in the first place.
toString() - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
toString() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.BagTableToRemove
Returns the SQL statement that will drop the table.
toString() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
toString() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
toString() - Method in class org.intermine.objectstore.proxy.ProxyCollection
We override this here in order to prevent possible infinite recursion.
toString() - Method in class org.intermine.objectstore.proxy.ProxyReference
toString() - Method in class org.intermine.objectstore.query.ClobAccess
Converts the Clob into a String.
toString() - Method in class org.intermine.objectstore.query.ConstraintSet
toString() - Method in class org.intermine.objectstore.query.ContainsConstraint
toString() - Method in class org.intermine.objectstore.query.iql.IqlQuery
Return a string version of the IqlQuery
toString() - Method in class org.intermine.objectstore.query.OverlapConstraint
toString() - Method in class org.intermine.objectstore.query.OverlapRange
toString() - Method in class org.intermine.objectstore.query.PendingClob
Converts the Clob into a String.
toString() - Method in class org.intermine.objectstore.query.Query
Returns a string representation of this Query object
toString() - Method in class org.intermine.objectstore.query.QueryClass
Returns a String representation.
toString() - Method in class org.intermine.objectstore.query.QueryClassBag
Returns a String representation.
toString() - Method in class org.intermine.objectstore.query.QueryField
Produces a String, for debugging purposes.
toString() - Method in class org.intermine.objectstore.query.QueryObjectReference
toString() - Method in class org.intermine.objectstore.query.QueryValue
toString() - Method in class org.intermine.objectstore.query.Results
 
toString() - Method in class org.intermine.objectstore.query.ResultsInfo
toString() - Method in class org.intermine.objectstore.query.SimpleConstraint
toString() - Method in class org.intermine.objectstore.query.UnknownTypeValue
toString() - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
toString() - Method in class org.intermine.pathquery.LogicExpression.Operator
Produce an expression for this branch of the tree.
toString() - Method in class org.intermine.pathquery.LogicExpression
Get the expression as a string.
toString() - Method in class org.intermine.pathquery.LogicExpression.Variable
Just returns the variable name.
toString() - Method in class org.intermine.pathquery.Node
toString() - Method in class org.intermine.pathquery.OrderElement
toString() - Method in class org.intermine.pathquery.Path
Returns a representation of the Path as a String, with class constraint markers.
toString() - Method in class org.intermine.pathquery.PathConstraintAttribute
toString() - Method in class org.intermine.pathquery.PathConstraintBag
toString() - Method in class org.intermine.pathquery.PathConstraintIds
toString() - Method in class org.intermine.pathquery.PathConstraintLookup
toString() - Method in class org.intermine.pathquery.PathConstraintLoop
toString() - Method in class org.intermine.pathquery.PathConstraintMultiValue
toString() - Method in class org.intermine.pathquery.PathConstraintNull
toString() - Method in class org.intermine.pathquery.PathConstraintSubclass
toString() - Method in class org.intermine.pathquery.PathQuery
Converts this object into a rudimentary String format, containing all the data.
toString() - Method in class org.intermine.sql.Database
toString() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
toString() - Method in class org.intermine.sql.precompute.PrecomputedTable
toString() - Method in class org.intermine.sql.query.Constant
toString() - Method in class org.intermine.sql.query.Constraint
toString() - Method in class org.intermine.sql.query.ExplainResult
toString() - Method in class org.intermine.sql.query.OrderDescending
toString() - Method in class org.intermine.sql.query.Query
Overrides Object.toString().
toString() - Method in class org.intermine.sql.query.Table
A toString method, which helps us when debugging.
toString() - Method in class org.intermine.template.TemplateQuery
 
toString() - Method in class org.intermine.template.TemplateValue
toString() - Method in class org.intermine.util.AlwaysSet
toString() - Method in class org.intermine.util.IntPresentSet
toString() - Method in class org.intermine.util.IntToIntMap
toString() - Method in class org.intermine.util.ReferenceMap
toString() - Method in class org.intermine.web.logic.config.Displayer
Return an XML String of this Type object
toString(String) - Method in class org.intermine.web.logic.config.Displayer
Return an XML String of this Type object
toString() - Method in class org.intermine.web.logic.config.FieldConfig
toString() - Method in class org.intermine.web.logic.config.TableExportConfig
toString() - Method in class org.intermine.web.logic.config.Type
Return an XML String of this Type object
toString() - Method in class org.intermine.web.logic.config.WebConfig
Return an XML String of this WebConfig object
toString() - Method in class org.intermine.web.logic.query.MetadataNode
toString() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns a representation of the Path as a String, with class constraint markers.
toString() - Method in class org.intermine.web.logic.results.InlineList
toString() - Method in class org.intermine.web.logic.template.ConstraintInput
 
toString() - Method in class org.intermine.web.logic.TreeNode
toString() - Method in class org.intermine.web.logic.WebUtil.HeadResource
 
toString() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
Return an XML String of this Type object
toString() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
Return an XML String of this Type object
toString() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
 
toString() - Method in class org.intermine.web.struts.oauth2.MigrationMapping
 
toString() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
toString() - Method in class org.intermine.web.tags.table.NavigationBarTag
 
toString() - Method in class org.intermine.webservice.client.core.ContentType
 
toString() - Method in class org.intermine.webservice.client.core.RequestImpl
 
toString() - Method in class org.intermine.webservice.client.core.Version
Returns string representation of Version that is send with request.
toString() - Method in class org.intermine.webservice.client.lists.ItemList
 
toString() - Method in class org.intermine.webservice.client.results.Item
 
toString() - Method in class org.intermine.webservice.server.core.Either.Left
 
toString() - Method in class org.intermine.webservice.server.core.Either.Right
 
toString() - Method in class org.intermine.webservice.server.core.Pair
 
toString() - Method in class org.intermine.webservice.server.core.SubTable
 
toString() - Method in class org.intermine.webservice.server.core.TableCell
 
toString() - Method in enum org.intermine.webservice.server.Format
 
toString() - Method in class org.intermine.webservice.server.JWTBuilder
 
toString() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
toString() - Method in class org.intermine.xml.full.Item
toStringNoConstraints() - Method in class org.intermine.pathquery.Path
Returns a representation of the Path as a String, with no class constraint markers.
toStrings(Collection<Integer>) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Convert a set of Integers to a set of String using idToIdentifier()
toStrings(List<Object>) - Method in class org.intermine.pathquery.PathQueryHandler
Convert a List of Objects to a List of Strings using toString
toStringTruncateParameters(int) - Method in class org.intermine.objectstore.query.iql.IqlQuery
Return a string version of the IqlQuery but truncated the parameters (lists of bag contents) to the specified length.
toXml() - Method in class org.intermine.pathquery.PathQuery
Convert a PathQuery to XML, using the default value of PathQuery.USERPROFILE_VERSION
toXml(int) - Method in class org.intermine.pathquery.PathQuery
Convert a PathQuery to XML.
toXml(int) - Method in class org.intermine.template.TemplateQuery
Convert a template query to XML.
TRAC_TICKET_URL_PREFIX - Static variable in class org.intermine.task.AcceptanceTestTask
Prefix of the ticket pages in Trac.
Track - Interface in org.intermine.api.tracker.track
Class representing the track
TrackAbstract - Class in org.intermine.api.tracker.track
long Class representing the track
TrackAbstract() - Constructor for class org.intermine.api.tracker.track.TrackAbstract
 
TrackAjaxServices - Class in org.intermine.dwr
 
TrackAjaxServices() - Constructor for class org.intermine.dwr.TrackAjaxServices
Construct a ajax services object that does tracking stuff.
Tracker - Interface in org.intermine.api.tracker
Interface to represent a Tracker, an object tracking the users activities in the webapp into the database
trackerDelegate - Variable in class org.intermine.api.InterMineAPI
 
TrackerDelegate - Class in org.intermine.api.tracker
Intermediate class which decouples the tracker components from the code that uses them.
TrackerDelegate(String[], ObjectStoreWriter) - Constructor for class org.intermine.api.tracker.TrackerDelegate
Create the tracker manager managing the trackers specified in input
TrackerFactory - Class in org.intermine.api.tracker.factory
Factory to instantiate the trackers with the reflection
trackerLogger - Variable in class org.intermine.api.tracker.AbstractTracker
 
TrackerLogger - Class in org.intermine.api.tracker
Runnable object providing insertion into the database.
TrackerLogger(Connection, Queue<Track>) - Constructor for class org.intermine.api.tracker.TrackerLogger
Construct a TrackerLogger for a specific connection and table
trackerLoggerThread - Variable in class org.intermine.api.tracker.TrackerDelegate
 
trackerMissingClasses - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
 
trackers - Variable in class org.intermine.api.tracker.TrackerDelegate
 
TrackerUtil - Class in org.intermine.api.tracker.util
 
TrackHandler - Class in org.intermine.api.tracker.xml
 
TrackHandler(ObjectStoreWriter) - Constructor for class org.intermine.api.tracker.xml.TrackHandler
 
trackKeywordSearch(String, Profile, String) - Method in class org.intermine.api.tracker.TrackerDelegate
Store into the database the login event
trackList(String, int, ListBuildMode, ListTrackerEvent, Profile, String) - Method in class org.intermine.api.tracker.ListTracker
 
trackListCreation(String, int, ListBuildMode, Profile, String) - Method in class org.intermine.api.tracker.TrackerDelegate
Store into the database the list creation
trackListExecution(String, int, Profile, String) - Method in class org.intermine.api.tracker.TrackerDelegate
Store into the database the list execution
trackLogin(String) - Method in class org.intermine.api.tracker.LoginTracker
Track when the user logs in his account
trackLogin(String) - Method in class org.intermine.api.tracker.TrackerDelegate
Store into the database the login event
TrackManagerBinding - Class in org.intermine.api.tracker.xml
Code for reading and writing all tracks objects as XML
TrackManagerHandler - Class in org.intermine.api.tracker.xml
Event handler for the track xml file
TrackManagerHandler(ObjectStoreWriter) - Constructor for class org.intermine.api.tracker.xml.TrackManagerHandler
Create a new TrackHandler
trackQuery(String, Profile, String) - Method in class org.intermine.api.tracker.QueryTracker
 
trackQuery(String, Profile, String) - Method in class org.intermine.api.tracker.TrackerDelegate
Store into the database the execution of a query (saved or temporary)
trackQueue - Variable in class org.intermine.api.tracker.AbstractTracker
 
trackSearch(String, Profile, String) - Method in class org.intermine.api.tracker.KeySearchTracker
Record the search.
trackTableName - Variable in class org.intermine.api.tracker.AbstractTracker
 
trackTemplate(String, Profile, String) - Method in class org.intermine.api.tracker.TemplateTracker
Store into the database the template execution by the user or if the user is not logged during a specific http session.
trackTemplate(String, Profile, String) - Method in class org.intermine.api.tracker.TrackerDelegate
Store into the database the template execution by the user specified in input
TransferInterruptedException - Exception in org.intermine.webservice.client.exceptions
TransferInterruptedException is the error thrown when a service returns an incomplete result set.
TransferInterruptedException(String) - Constructor for exception org.intermine.webservice.client.exceptions.TransferInterruptedException
 
TransferInterruptedException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.TransferInterruptedException
 
TransferInterruptedException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.TransferInterruptedException
 
TransferInterruptedException() - Constructor for exception org.intermine.webservice.client.exceptions.TransferInterruptedException
Construct a new TransferInterrupted Exception.
TransferSequences - Class in org.intermine.bio.postprocess
Transfer sequences from the Assembly objects to the other objects that are located on the Assemblys and to the objects that the Assemblys are located on (eg.
TransferSequences(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.TransferSequences
Create a new TransferSequences object from the given ObjectStoreWriter
transferToLocatedSequenceFeatures() - Method in class org.intermine.bio.postprocess.TransferSequences
Use the Location relations to copy the sequence from the Chromosomes to every SequenceFeature that is located on a Chromosome and which doesn't already have a sequence (ie. don't copy to Assembly).
transferToTranscripts() - Method in class org.intermine.bio.postprocess.TransferSequences
For each Transcript, join and transfer the sequences from the child Exons to a new Sequence object for the Transcript.
transform(Object) - Method in class org.intermine.api.profile.TagMapper
 
transform(Tag) - Method in class org.intermine.api.profile.TagMapper
Transform a tag into a string of some kind.
translate(char) - Method in class org.intermine.bio.util.ClobAccessReverseComplement
Translates a single character to the complement base for DNA.
translateFromDbObject(Object) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Translate an object exiting the ObjectStore.
translateFromDbObject(Object) - Method in class org.intermine.objectstore.translating.Translator
Translate an object exiting the ObjectStore.
translateIdToIdentifier(Integer) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Translate an object id into a native identifier.
translateIdToIdentifier(Integer) - Method in class org.intermine.objectstore.translating.Translator
Translate an object id into a native identifier.
translateQuery(Query) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Translate a query.
translateQuery(Query) - Method in class org.intermine.objectstore.translating.Translator
Translate a query.
translateToDbObject(Object) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Translate an object entering the ObjectStore.
translateToDbObject(Object) - Method in class org.intermine.objectstore.translating.Translator
Translate an object entering the ObjectStore.
Translator - Class in org.intermine.objectstore.translating
Interface specifying operations required for inline translation of queries and data objects by a translating ObjectStore.
Translator() - Constructor for class org.intermine.objectstore.translating.Translator
 
traverseConstraint(Constraint, Map<QueryEvaluable, ConstraintSet>) - Method in class org.intermine.api.bag.BagQuery
Finds all BagConstraints in a Constraint, and places the QueryEvaluable and the containing ConstraintSet into the given Map.
traverseConstraints(Constraint, ConstraintTraverseAction) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Traverse the given Constraint tree (ie. recursively look for nested constraints if the argument is a ConstraintSet) and call ConstraintTraverseAction for each Constraint.
TreatStringTag - Class in org.intermine.web.tags.util
Tag escaping apostrophes, quotes and replacing "\n" with html tag for end of line.
TreatStringTag() - Constructor for class org.intermine.web.tags.util.TreatStringTag
 
TreeAction - Class in org.intermine.web.struts
Implementation of Action that modifies a tree.
TreeAction() - Constructor for class org.intermine.web.struts.TreeAction
 
TreeController - Class in org.intermine.web.struts
Perform initialisation steps for displaying a tree
TreeController() - Constructor for class org.intermine.web.struts.TreeController
 
TreefamConverter - Class in org.intermine.bio.dataconversion
 
TreefamConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.TreefamConverter
Constructor
TreefamConverter.GeneHolder - Class in org.intermine.bio.dataconversion
temporary object that holds the id, identifier, symbol, and gene for each record
TreefamConverter.GeneHolder(String, String, String, String, String, String) - Constructor for class org.intermine.bio.dataconversion.TreefamConverter.GeneHolder
 
TreeNode - Class in org.intermine.web.logic
Bean to represent one row in the display of a tree
TreeNode(Object, String, int, boolean, boolean, boolean, List<String>) - Constructor for class org.intermine.web.logic.TreeNode
Constructor
TreeWalker<L> - Class in org.intermine.webservice.server.core
A type alias to reduce type stuttering.
TreeWalker() - Constructor for class org.intermine.webservice.server.core.TreeWalker
 
TriageBagAction - Class in org.intermine.web.struts
An action to handle reparative actions to bags.
TriageBagAction() - Constructor for class org.intermine.web.struts.TriageBagAction
 
TriageBagForm - Class in org.intermine.web.struts
 
TriageBagForm() - Constructor for class org.intermine.web.struts.TriageBagForm
 
trimLeft(String) - Static method in class org.intermine.metadata.StringUtil
trim left space in string
trimSlashes(String) - Static method in class org.intermine.metadata.StringUtil
Trim starting and trailing '/' characters from a string if present.
TRUE - Static variable in class org.intermine.objectstore.query.QueryValue
The true value
TRUNCATED_CLASSES - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key used to store the truncated classes string.
TSVFileReaderTask - Class in org.intermine.task
Read a file of tab separated values.
TSVFileReaderTask() - Constructor for class org.intermine.task.TSVFileReaderTask
 
type - Variable in class org.intermine.api.results.Column
 
type - Variable in class org.intermine.bio.dataconversion.UniprotEntry.Comment
 
type - Variable in class org.intermine.metadata.AttributeDescriptor
 
type - Variable in class org.intermine.objectstore.query.QueryReference
 
type(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be a particular subclass (type).
type - Variable in class org.intermine.task.ModelOutputTask
 
Type - Class in org.intermine.web.logic.config
Configuration object for displaying a class
Type() - Constructor for class org.intermine.web.logic.config.Type
 
TYPE_BOOLEAN - Static variable in class org.intermine.objectstore.query.UnknownTypeValue
A value that indicates that the value represents a Boolean.
TYPE_CONVERTED - Static variable in class org.intermine.api.bag.BagQueryResult
Key of the Map returned by getIssues() when the object found when querying using input string needed to be translated.
TYPE_NUMBER - Static variable in class org.intermine.objectstore.query.UnknownTypeValue
A value that indicates that the value represents a number.
TYPE_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
The type of the list
TYPE_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListsRequestParser
Name of parameter with object type.
TYPE_PARAMETER - Static variable in class org.intermine.webservice.server.template.result.TemplateResultService
Name of type parameter
TYPE_STRING - Static variable in class org.intermine.objectstore.query.UnknownTypeValue
A value that indicates that the value represents a String or Date.
TYPECAST - Static variable in class org.intermine.sql.query.Function
Type casts - takes two operands.
typeConstraintToJson(PathConstraint) - Method in class org.intermine.pathquery.PathQuery
format a type constraint to a JSON representation.
TypeConverter - Class in org.intermine.api.bag
Static helper routines to convert bags between different types.
types - Variable in class org.intermine.bio.ontology.OboParser
All relation types
TYPES - Static variable in class org.intermine.bio.web.model.GeneModel
The unqualified class names of types that comprise a gene model.
types - Variable in class org.intermine.sql.precompute.PrecomputedTableManager
 
TYPES - Static variable in class org.intermine.web.logic.config.HeaderConfigTitle
The parts that make up a header (main title, sub title)
TypeUtil - Class in org.intermine.metadata
Provides utility methods for working with Java types and reflection
TypeUtil.FieldInfo - Class in org.intermine.metadata
Inner class to hold info on a field.
TypeUtil.FieldInfo(String, Method, Method, Method, Method, Method) - Constructor for class org.intermine.metadata.TypeUtil.FieldInfo
Construct a new FieldInfo object.

U

unaccept() - Method in class org.intermine.api.bag.SharingInvite
 
UnauthorizedException - Exception in org.intermine.webservice.server.exceptions
 
UnauthorizedException() - Constructor for exception org.intermine.webservice.server.exceptions.UnauthorizedException
Construct an UnauthorizedException
UnauthorizedException(String) - Constructor for exception org.intermine.webservice.server.exceptions.UnauthorizedException
 
unescape(String) - Method in class org.intermine.bio.ontology.OboParser
Perform OBO unescaping.
unescape(String) - Static method in class org.intermine.objectstore.query.iql.IqlQueryParser
Unescapes a String, by removing quotes from the beginning and end.
UnhandledFeatureException - Exception in org.intermine.api.query.codegen
Exception representing the failure to encode a feature in the target language.
UnhandledFeatureException() - Constructor for exception org.intermine.api.query.codegen.UnhandledFeatureException
Create an exception with a default message.
UnhandledFeatureException(String) - Constructor for exception org.intermine.api.query.codegen.UnhandledFeatureException
Create an exception with a given message.
UnhandledFeatureException(Throwable) - Constructor for exception org.intermine.api.query.codegen.UnhandledFeatureException
Create an exception when there is something to blame.
UnhandledFeatureException(String, Throwable) - Constructor for exception org.intermine.api.query.codegen.UnhandledFeatureException
Create an exception when there is a message and a cause
UNION - Static variable in class org.intermine.api.bag.BagOperations
Constant representing logical union.
union(Model, Collection<InterMineBag>, String, Profile, ClassKeys) - Static method in class org.intermine.api.bag.BagOperations
Create a bag that is the UNION of all the bags provided, if the union is the empty set then don't create the new bag - if bags are of incompatible types or are all empty.
Union - Class in org.intermine.api.bag.operations
 
Union(Model, Profile, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.Union
 
UNION - Static variable in class org.intermine.objectstore.query.ObjectStoreBagCombination
Constant representing a UNION operation
UniProtCommentsDisplayer - Class in org.intermine.bio.web.displayer
metabolicMine UniProt curated comments displayer on Gene report page
UniProtCommentsDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.UniProtCommentsDisplayer
Construct with config and the InterMineAPI.
UniprotConfig - Class in org.intermine.bio.dataconversion
 
UniprotConfig() - Constructor for class org.intermine.bio.dataconversion.UniprotConfig
read configuration file
UniprotConfig.ConfigEntry - Class in org.intermine.bio.dataconversion
class representing an organism in the uniprot config file
UniprotConfig.ConfigEntry() - Constructor for class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
 
UniprotConfig.IdentifierConfig - Class in org.intermine.bio.dataconversion
class representing a line in the uniprot config file
UniprotConfig.IdentifierConfig(String, String) - Constructor for class org.intermine.bio.dataconversion.UniprotConfig.IdentifierConfig
 
UniprotConverter - Class in org.intermine.bio.dataconversion
DataConverter to parse UniProt data into items.
UniprotConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.UniprotConverter
Constructor
UniprotConverter.DiseaseHolder - Class in org.intermine.bio.dataconversion
temporarily hold disease item until stored
UniprotConverter.DiseaseHolder() - Constructor for class org.intermine.bio.dataconversion.UniprotConverter.DiseaseHolder
Constructor
UniprotEntry - Class in org.intermine.bio.dataconversion
holder class representing an entry in uniprot xml
UniprotEntry() - Constructor for class org.intermine.bio.dataconversion.UniprotEntry
constructor used for non-isoform entries
UniprotEntry(String) - Constructor for class org.intermine.bio.dataconversion.UniprotEntry
 
UniprotEntry.Comment - Class in org.intermine.bio.dataconversion
Class representing a comment in a uniprot entry.
UniprotEntry.Comment(String) - Constructor for class org.intermine.bio.dataconversion.UniprotEntry.Comment
 
UniprotEntry.Dbref - Class in org.intermine.bio.dataconversion
class representing a dbref entry in a uniprot entry
UniprotEntry.Dbref(String, String) - Constructor for class org.intermine.bio.dataconversion.UniprotEntry.Dbref
 
UniProtFastaLoaderTask - Class in org.intermine.bio.dataconversion
Code for loading fasta for uniprot proteins.
UniProtFastaLoaderTask() - Constructor for class org.intermine.bio.dataconversion.UniProtFastaLoaderTask
 
UniprotFilterTask - Class in org.intermine.bio.dataconversion
Read a set of Uniprot XML files and write out only those elements for an organism in the given set of names.
UniprotFilterTask() - Constructor for class org.intermine.bio.dataconversion.UniprotFilterTask
 
UniprotKeywordConverter - Class in org.intermine.bio.dataconversion
Importer to add descriptions to UniProt keywords
UniprotKeywordConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.UniprotKeywordConverter
Constructor
UniprotXmlFilter - Class in org.intermine.bio.dataconversion
Extract only entries for organisms of interest from UniProt XML dump files.
UniprotXmlFilter(Set) - Constructor for class org.intermine.bio.dataconversion.UniprotXmlFilter
Construct a filter with a set of organism full names to extract entries for.
UNIQUE_INTEGER_SEQUENCE_NAME - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the SEQUENCE in the database to use when generating unique integers in getUniqueInteger().
UNIQUE_KEYS - Static variable in class org.intermine.api.profile.UserPreferences
Common keys
uniqueColumnValues(PathQuery, String) - Method in class org.intermine.api.query.QueryExecutor
Get the the total number of unique column values for a given path in the context of a given query.
uniqueId - Variable in class org.intermine.bio.dataconversion.OboConverter
 
uniqueString() - Static method in class org.intermine.metadata.StringUtil
Returns a String that is different every time
uniqueSynId - Variable in class org.intermine.bio.dataconversion.OboConverter
 
UNIX_SEPARATOR - Static variable in interface org.intermine.web.logic.export.Exporter
Unix line separator only LF
UnknownBagTypeException - Exception in org.intermine.api.bag
Exception thrown when given attempting to create a bag for a type that isn't in the model, this can happen when reading bags from a userprofile database and the data model has changed.
UnknownBagTypeException(String) - Constructor for exception org.intermine.api.bag.UnknownBagTypeException
Constructs an IncompatibleBagTypesException with the specified detail message.
UnknownBagTypeException(Throwable) - Constructor for exception org.intermine.api.bag.UnknownBagTypeException
Constructs an IncompatibleBagTypesException with the specified nested throwable.
UnknownBagTypeException(String, Throwable) - Constructor for exception org.intermine.api.bag.UnknownBagTypeException
Constructs an IncompatibleBagTypesException with the specified detail message and nested throwable.
UnknownTypeValue - Class in org.intermine.objectstore.query
Represents a value with an unknown type.
UnknownTypeValue(String) - Constructor for class org.intermine.objectstore.query.UnknownTypeValue
Constructor.
unmarhsal(InputStream) - Static method in class org.intermine.web.logic.aspects.AspectBinding
Read data set configuration from an input stream.
unmarshal(Reader, ObjectStoreWriter) - Static method in class org.intermine.api.tracker.xml.TemplateTrackBinding
Read the template tracks from an XML stream Reader.
unmarshal(Reader, ObjectStoreWriter, ObjectStoreWriter, Integer) - Static method in class org.intermine.api.xml.InterMineBagBinding
Parse saved queries from a Reader
unmarshal(Reader, ProfileManager, String, String, Set<Tag>, ObjectStoreWriter, int) - Static method in class org.intermine.api.xml.ProfileBinding
Read a Profile from an XML stream Reader.
unmarshal(Reader, ProfileManager, ObjectStoreWriter, boolean) - Static method in class org.intermine.api.xml.ProfileManagerBinding
Read a ProfileManager from an XML stream Reader
unmarshal(Reader, ProfileManager, ObjectStoreWriter) - Static method in class org.intermine.api.xml.ProfileManagerBinding
Read a ProfileManager from an XML stream Reader.
unmarshal(Reader, Map, int) - Static method in class org.intermine.api.xml.SavedQueryBinding
Parse TemplateQuerys from XML
unmarshal(Reader, Integer) - Static method in class org.intermine.api.xml.SharedBagBinding
Parse saved queries from a Reader.
unmarshal(ProfileManager, String, Reader) - Method in class org.intermine.api.xml.TagBinding
Parse Tags from XML and write them to the userprofile object store
unmarshal(InputStream) - Method in class org.intermine.util.XmlBinding
Unmarshal an XML file to an object.
unmarshal(Reader) - Static method in class org.intermine.web.logic.aspects.AspectBinding
Read in data set configuration from XML.
unmarshall(File) - Static method in class org.intermine.task.project.ProjectXmlBinding
Create a Project object from a project.xml file.
unmarshalPathQueries(Reader, int) - Static method in class org.intermine.pathquery.PathQueryBinding
Parse PathQueries from XML.
unmarshalPathQueries(Reader, int, Model) - Static method in class org.intermine.pathquery.PathQueryBinding
Parse PathQueries from XML, declaring which model should be used in preference to the default model retrieved by Model::getInstanceByName.
unmarshalPathQuery(Reader, int) - Static method in class org.intermine.pathquery.PathQueryBinding
Parses PathQuery from XML.
unmarshalPathQuery(Reader, int, Model) - Static method in class org.intermine.pathquery.PathQueryBinding
Parses a PathQuery from XML, declaring which model should be used in preference to the default model retrieved by Model::getInstanceByName.
unmarshalTemplates(Reader, int) - Static method in class org.intermine.template.xml.TemplateQueryBinding
Parse TemplateQueries from XML.
unqualifiedName(String) - Static method in class org.intermine.metadata.TypeUtil
Returns the unqualified class name from a fully qualified class name
unqualifiedName(String) - Static method in class org.intermine.metadata.Util
Returns the unqualified class name from a fully qualified class name
unshareAllBagsFromUser(Profile, Profile) - Method in class org.intermine.api.bag.SharedBagManager
Stop sharing all bags owned by the given user which have been shared with the given recipient.
unshareBagWithAllUsers(StorableBag) - Method in class org.intermine.api.bag.SharedBagManager
Delete the sharing between the bag and all the users sharing the bag.
unshareBagWithUser(String, String, String) - Method in class org.intermine.api.bag.BagManager
Unshare the bag with the user given in input
unshareBagWithUser(InterMineBag, Profile) - Method in class org.intermine.api.bag.BagManager
Un-share the bag with the user given in input
unshareBagWithUser(InterMineBag, String) - Method in class org.intermine.api.bag.SharedBagManager
Delete the sharing between the user and the bag given in input
unverbosify(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails
Deprecated.
ajaxVerbosify is used instead
uosw - Variable in class org.intermine.api.bag.SharedBagManager
 
uosw - Variable in class org.intermine.api.profile.ProfileManager
 
upcast(Map<String, TemplateQuery>) - Static method in class org.intermine.api.template.TemplateHelper
Transform a map of templates into a map of API templates.
update() - Method in class org.intermine.api.profile.ModelUpdate
Update bags, savedquery and savedtemplatequery if class has been renamed -> update type bags, update savedquery and savedtemplatequery if a field has been renamed -> update savedquery and savedtemplatequery if class has been deleted -> delete bags with that type
update(Map<String, String>, Map<String, String>) - Method in class org.intermine.api.profile.PathQueryUpdate
Update the path query
updateBagType(String, String) - Method in class org.intermine.api.profile.Profile
Update the type of bag.
updateColumnValue(Database, String, String, Object) - Static method in class org.intermine.sql.DatabaseUtil
Set the default value in a column for all values where the current value is null.
updateColumnValue(Connection, String, String, Object) - Static method in class org.intermine.sql.DatabaseUtil
Set the default value in a column for all values.
updateConstraints(Map<String, String>, Map<String, String>) - Method in class org.intermine.api.profile.PathQueryUpdate
Update the constraint with the renamed classes or/and fields
updateConstraints(Map<String, String>, Map<String, String>) - Method in class org.intermine.api.profile.TemplateQueryUpdate
 
UpdateListTablesTask - Class in org.intermine.web.task
Task that rename the column 'intermine_current' into 'intermine_state' in savedbag table (from boolean to text) and add the column 'extra' (and its value) in the bagvalues table
UpdateListTablesTask() - Constructor for class org.intermine.web.task.UpdateListTablesTask
 
updatePopulationQuery(Query, Query, QueryField) - Method in class org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient
Update the annotated population query given in input using the queryfield specific for the correction
updatePopulationQuery(Query, Query, QueryField) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient
Update the annotated population query given in input using the queryfield specific for the correction
updateQueryWithCorrectionCoefficient(Query, QueryClass) - Method in class org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient
Update the query, given in input, with the field associated with the correction coefficient and return a query field.
updateQueryWithCorrectionCoefficient(Query, QueryClass) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient
Update the query, given in input, with the field associated with the correction coefficient and return a query field.
updateReferredQueryAndTemplate() - Method in class org.intermine.api.profile.ModelUpdate
Update savedquery and savedtemplatequery when they reeferring to renamed classes or fields
updateStatistics(Map<String, Integer>, Connection) - Method in interface org.intermine.sql.writebatch.BatchWriter
Updates the per-table statistics held in this object, and may tell the SQL database to update its statistics using the supplied Connection.
updateStatistics(Map<String, Integer>, Connection) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Updates the per-table statistics held in this object, and may tell the SQL database to update its statistics using the supplied Connection.
updateTags() - Method in class org.intermine.webservice.client.lists.ItemList
Make sure that the tags on this object are up-to-date with those stored on the server.
updateTemplate(String, ApiTemplate) - Method in class org.intermine.api.profile.Profile
Update an existing template, throw exceptions when template doesn't exist.
updateTemplate(String, String) - Method in class org.intermine.dwr.AjaxServices
Update with the value given in input the field of the previous template saved into the session
updateTemplateName(String, String, Connection) - Method in class org.intermine.api.tracker.TemplateTracker
Update the template name value into the database
updateTemplateName(String, String) - Method in class org.intermine.api.tracker.TrackerDelegate
Update the template name value into the database
UpdateTrackTableTask - Class in org.intermine.web.task
Task to modify the type of the column 'timestamp' in the templatetrack table in the userprofile database.
UpdateTrackTableTask() - Constructor for class org.intermine.web.task.UpdateTrackTableTask
 
updateTypeBag() - Method in class org.intermine.api.profile.ModelUpdate
Update the type to all bags having as a type one of the classes renamed
updateUserRepositoryWithSharedBags() - Method in class org.intermine.api.profile.Profile
Update the user repository with the sharedbags
updateUserRepositoryWithSharedBags() - Method in class org.intermine.api.search.UserRepository
Update the user repository with the shared bags
UpgradeBagList - Class in org.intermine.web.logic.profile
Runnable object providing upgrading osbag_int table.
UpgradeBagList(Profile, BagQueryRunner) - Constructor for class org.intermine.web.logic.profile.UpgradeBagList
Constructor
UpgradeJob - Class in org.intermine.api.idresolution
 
UpgradeJob(UUID, BagQueryUpgrade) - Constructor for class org.intermine.api.idresolution.UpgradeJob
 
upgradeOsb(Collection<Integer>, boolean) - Method in class org.intermine.api.profile.InterMineBag
Upgrades the ObjectStoreBag with a new ObjectStoreBag containing the collection of elements given in input
UPGRADING_BAG - Static variable in class org.intermine.web.logic.Constants
Key for the upgrading bag on the session
UPPER - Static variable in class org.intermine.objectstore.query.QueryExpression
Upper case version of the given string
UPPER - Static variable in class org.intermine.sql.query.Function
UPPER operator - takes one operand
URLGenerator - Class in org.intermine.web.util
Class generating useful links like base link: http://localhost:8080/query
URLGenerator(HttpServletRequest) - Constructor for class org.intermine.web.util.URLGenerator
Constructor.
URLParser - Class in org.intermine.webservice.client.util
The URLParse class is util class for parsing URL.
URLUtil - Class in org.intermine.web.util
Util class for URL processing.
USAGE - Static variable in class org.intermine.webservice.server.lists.ListDeletionService
Usage information to help users who provide incorrect input.
USAGE - Static variable in class org.intermine.webservice.server.lists.ListRenameService
Usage information to help users who provide incorrect input.
USAGE - Static variable in class org.intermine.webservice.server.lists.ListUploadService
A usage string to return for bad requests.
useJoin - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
USER - Static variable in class org.intermine.api.search.Scope
User scope for private bags, templates, etc.
user - Variable in class org.intermine.task.GrantTask
 
USER_BAGS - Static variable in class org.intermine.api.search.SearchTarget
The search target for user bags
USER_TEMPLATES - Static variable in class org.intermine.api.search.SearchTarget
The search target for user templates
UserAlreadyShareBagException - Exception in org.intermine.api.profile
Exception thrown when a user already shares the bag.
UserAlreadyShareBagException() - Constructor for exception org.intermine.api.profile.UserAlreadyShareBagException
Constructor
UserAlreadyShareBagException(String) - Constructor for exception org.intermine.api.profile.UserAlreadyShareBagException
Constructor with message.
UserAlreadyShareBagException(Throwable) - Constructor for exception org.intermine.api.profile.UserAlreadyShareBagException
Constructor with throwable
UserAlreadyShareBagException(String, Throwable) - Constructor for exception org.intermine.api.profile.UserAlreadyShareBagException
Constructor with message and throwable
UserAlreadyShareBagException(SavedBag, UserProfile) - Constructor for exception org.intermine.api.profile.UserAlreadyShareBagException
Constructor with the actual objects we are trying to link.
useRangeTypes - Variable in class org.intermine.objectstore.intermine.DatabaseSchema
 
useRangeTypes() - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns true if we can use Postgres built-in range types on this database.
UserDataFormatter - Class in org.intermine.webservice.server.user
A class that processes information about a user into XML.
UserDataFormatter() - Constructor for class org.intermine.webservice.server.user.UserDataFormatter
 
userId - Variable in class org.intermine.api.profile.Profile
 
username - Variable in class org.intermine.api.profile.Profile
 
userName - Variable in class org.intermine.api.tracker.track.TrackAbstract
 
USERNAME - Static variable in class org.intermine.api.util.AnonProfile
The user name of the anonymous user.
USERNAME - Static variable in class org.intermine.web.logic.Constants
The display name of the current user
username - Variable in class org.intermine.web.struts.CreateAccountForm
 
username - Variable in class org.intermine.web.struts.LoginForm
 
username - Variable in class org.intermine.web.struts.RequestPasswordForm
 
username - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
UserNotFoundException - Exception in org.intermine.api.profile
Exception thrown when user is not found.
UserNotFoundException(String) - Constructor for exception org.intermine.api.profile.UserNotFoundException
Constructor with message.
UserNotFoundException(Throwable) - Constructor for exception org.intermine.api.profile.UserNotFoundException
Constructor with throwable
UserNotFoundException(String, Throwable) - Constructor for exception org.intermine.api.profile.UserNotFoundException
Constructor with message and nested exception.
UserPreferences - Class in org.intermine.api.profile
 
UserPreferences(PreferencesManager, Profile) - Constructor for class org.intermine.api.profile.UserPreferences
 
USERPROFILE_VERSION - Static variable in class org.intermine.pathquery.PathQuery
Version number for the userprofile and PathQuery XML format.
userProfileAlias - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
userProfileOS - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
UserProperty - Class in org.intermine.task.project
Bean to hold property elements from project.xml files.
UserProperty() - Constructor for class org.intermine.task.project.UserProperty
 
UserRepository - Class in org.intermine.api.search
A repository for searching the searchable items of a single user.
UserRepository(Profile) - Constructor for class org.intermine.api.search.UserRepository
Constructor.
UsersController - Class in org.intermine.web.struts
Controller for the users admin page
UsersController() - Constructor for class org.intermine.web.struts.UsersController
 
UserTemplateAction - Class in org.intermine.web.struts
Make some change to a user template.
UserTemplateAction() - Constructor for class org.intermine.web.struts.UserTemplateAction
 
Util - Class in org.intermine.metadata
Generic utility functions.

V

v - Variable in class org.intermine.sql.query.SelectValue
 
VALID_OPS - Static variable in class org.intermine.objectstore.query.BagConstraint
List of possible operations
VALID_OPS - Static variable in class org.intermine.objectstore.query.ClassConstraint
Valid operators for this constraint.
VALID_OPS - Static variable in class org.intermine.objectstore.query.ConstraintSet
 
VALID_OPS - Static variable in class org.intermine.objectstore.query.ContainsConstraint
List of possible operations
VALID_OPS - Static variable in class org.intermine.objectstore.query.SubqueryConstraint
 
VALID_OPS - Static variable in class org.intermine.objectstore.query.SubqueryExistsConstraint
 
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintAttribute
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintBag
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintIds
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintLoop
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintMultitype
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintMultiValue
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintNull
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintRange
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintSubclass
List of valid ops for this type of constraint
VALID_OPS_NULL - Static variable in class org.intermine.objectstore.query.ContainsConstraint
List of possible null operations
VALID_TYPES - Static variable in class org.intermine.metadata.AttributeDescriptor
This is a list of the valid type strings.
validate() - Method in class org.intermine.api.tracker.track.KeySearchTrack
 
validate() - Method in class org.intermine.api.tracker.track.ListTrack
Validate the track before saving into the database
validate() - Method in class org.intermine.api.tracker.track.LoginTrack
Validate the track before saving into the database
validate() - Method in class org.intermine.api.tracker.track.QueryTrack
 
validate() - Method in class org.intermine.api.tracker.track.TemplateTrack
Validate the track before saving into the database
validate() - Method in interface org.intermine.api.tracker.track.Track
Validate the track before saving into the database
validate(File) - Method in class org.intermine.task.project.Project
Validate contents of a project.xml file once it has been unmarshalled.
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ChangePasswordForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ContactForm
When there are no other errors, check email address is valid.
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.CreateAccountForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ImportQueriesForm
Call inherited method then check whether xml is valid.
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.LoginForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyQueryForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyTemplateForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.PasswordResetForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.SaveQueryForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.TemplateSettingsForm
 
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.TemplatesImportForm
Call inherited method then check whether xml is valid.
validate(String, String) - Method in class org.intermine.webservice.server.query.result.XMLValidator
Validates an XML string according to an XML Schema at a given URL.
validateBagName(String) - Static method in class org.intermine.dwr.AjaxServices
validate bag upload
validateBagOperations(String, String[], String) - Static method in class org.intermine.dwr.AjaxServices
validation that happens before new bag is saved
validateForGroups(List<? extends Collection<String>>) - Method in class org.intermine.pathquery.LogicExpression
Validates an expression for the given groups of codes, making sure each group is only ANDed together.
validateGenomicRegions() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService
Validate input genomic regions
validateLookupConstraints() - Method in class org.intermine.template.TemplateQuery
Verify templates don't contain non-editable lookup constraints
validateName(Collection<String>, String) - Static method in class org.intermine.api.util.NameUtil
Checks that the name doesn't already exist and returns a numbered name if it does.
validateName(String) - Method in class org.intermine.pathquery.PathQueryHandler
Checks that the query has a name and that there's no name duplicates and appends a number to the name if there is.
validatePath(String, Model) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil
Path should be of the form: Class1 ref1 Class2 ref2 Class3 Where the number of elements is greater than one and an odd number.
validateRequiredParams() - Method in class org.intermine.webservice.server.lists.AsymmetricOperationInput
 
validateRequiredParams() - Method in class org.intermine.webservice.server.lists.CommutativeOperationInput
 
validateRequiredParams() - Method in class org.intermine.webservice.server.lists.ListInput
Check that the required parameters are there
validateRequiredParams() - Method in class org.intermine.webservice.server.lists.ListRenameInput
 
validateState() - Method in class org.intermine.bio.webservice.AbstractRegionExportService
 
validateState() - Method in class org.intermine.webservice.server.core.ReadWriteJSONService
 
validateState() - Method in class org.intermine.webservice.server.lists.AuthenticatedListService
 
validateState() - Method in class org.intermine.webservice.server.lists.ListMakerService
 
validateState() - Method in class org.intermine.webservice.server.query.QueryToListService
 
validateState() - Method in class org.intermine.webservice.server.query.QueryUploadService
 
validateState() - Method in class org.intermine.webservice.server.template.TemplateRemovalService
 
validateState() - Method in class org.intermine.webservice.server.template.TemplateUploadService
 
validateState() - Method in class org.intermine.webservice.server.user.DeregistrationService
 
validateState() - Method in class org.intermine.webservice.server.user.NewUserService
 
validateState() - Method in class org.intermine.webservice.server.user.WhoAmIService
 
validateState() - Method in class org.intermine.webservice.server.WebService
Subclasses can put initialisation checks here.
validateWidgetsConfig(Model) - Method in class org.intermine.web.logic.config.WebConfig
Validate the content (the paths) in the widget config
validChromosomes() - Static method in class org.intermine.bio.dataconversion.EnsemblIdResolverFactory
Get a set of valid chromosome identifiers for human as we want to ignore other data types
validComparison(Class<?>, ConstraintOp, Class<?>) - Static method in class org.intermine.objectstore.query.SimpleConstraint
Check whether a comparison is valid i.e. the arguments are comparable types and the the operator is permitted for those types
validGene() - Method in class org.intermine.bio.dataconversion.TreefamConverter.GeneHolder
 
validHomologue() - Method in class org.intermine.bio.dataconversion.TreefamConverter.GeneHolder
 
validOps - Variable in class org.intermine.objectstore.query.OverlapConstraint
 
validOps(Class<?>) - Static method in class org.intermine.objectstore.query.SimpleConstraint
Return the list of valid (binary) operator codes given arguments of a specified type
validPassword(String, String) - Method in class org.intermine.api.profile.ProfileManager
Validate a user's password A check should be made prior to this call to ensure a Profile exists
value - Variable in class org.intermine.sql.query.Constant
 
valueConstraintToJson(String, PathConstraint) - Method in class org.intermine.pathquery.PathQuery
Format a value constraint to a JSON representation.
valueEquals(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
Compare the value of this AbstractValue with another to see if it is equal.
valueMap - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
valueOf(String) - Static method in enum org.intermine.api.idresolution.Job.JobStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.lucene.KeywordSearchFacetType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.mines.ContentType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.profile.BagState
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.profile.ProfileManager.ApiPermission.Level
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.profile.TagMapper.Field
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.search.TaggingEvent.TagChange
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.tracker.util.ListBuildMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.tracker.util.ListTrackerEvent
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.bio.web.biojava.BioSequenceFactory.SequenceType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.pathquery.OrderDirection
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.pathquery.OuterJoinStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.sql.DatabaseUtil.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.template.SwitchOffAbility
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.template.TemplateValue.ValueType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.web.logic.widget.ErrorCorrection.Strategy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.web.logic.widget.GraphWidgetActionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.web.struts.oauth2.MessageFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.web.struts.oauth2.ResponseType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.webservice.client.core.Request.RequestType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.webservice.server.ColumnHeaderStyle
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.webservice.server.core.WebServiceServlet.Method
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.webservice.server.Format
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.webservice.server.jbrowse.Commands.Action
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.webservice.server.JWTBuilder.Algorithm
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.webservice.server.output.JSONRowResultProcessor.Verbosity
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.webservice.server.widget.WidgetProcessorImpl.WidgetType
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.intermine.api.idresolution.Job.JobStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.lucene.KeywordSearchFacetType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.mines.ContentType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.profile.BagState
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.profile.ProfileManager.ApiPermission.Level
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.profile.TagMapper.Field
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.search.TaggingEvent.TagChange
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.tracker.util.ListBuildMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.tracker.util.ListTrackerEvent
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.bio.web.biojava.BioSequenceFactory.SequenceType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.pathquery.OrderDirection
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.pathquery.OuterJoinStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.sql.DatabaseUtil.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.template.SwitchOffAbility
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.template.TemplateValue.ValueType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class org.intermine.util.AlwaysMap
values() - Method in class org.intermine.util.IdentityMap
values() - Method in class org.intermine.util.ReferenceMap
values() - Static method in enum org.intermine.web.logic.widget.ErrorCorrection.Strategy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.web.logic.widget.GraphWidgetActionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.web.struts.oauth2.MessageFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.web.struts.oauth2.ResponseType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.webservice.client.core.Request.RequestType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.webservice.server.ColumnHeaderStyle
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.webservice.server.core.WebServiceServlet.Method
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.webservice.server.Format
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.webservice.server.jbrowse.Commands.Action
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.webservice.server.JWTBuilder.Algorithm
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.webservice.server.output.JSONRowResultProcessor.Verbosity
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.webservice.server.widget.WidgetProcessorImpl.WidgetType
Returns an array containing the constants of this enum type, in the order they are declared.
VALUES_TEMPLATE - Static variable in class org.intermine.api.config.Constants
returns available queryable values for mine
VcfLoaderTask - Class in org.intermine.bio.dataconversion
Loader for VCF files
VcfLoaderTask() - Constructor for class org.intermine.bio.dataconversion.VcfLoaderTask
 
verboseException(Exception) - Static method in class org.intermine.metadata.Util
Takes an Exception, and returns an Exception of similar type with all available information in the message.
verboseQueryLog - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
verbosify(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails
Deprecated.
ajaxVerbosify is used instead
VERIFICATION_STRATEGY - Static variable in class org.intermine.webservice.server.JWTVerifier
The strategy used to verify tokens
verifiedSources - Static variable in class org.intermine.dataloader.DataLoaderHelper
 
verify(Model, String) - Static method in class org.intermine.dataloader.PriorityConfig
Verifies the priorities config given the list of data sources.
verify(String) - Method in class org.intermine.webservice.server.JWTVerifier
Verify this token and return a verification result.
VERIFYAUDIENCE - Static variable in class org.intermine.webservice.server.JWTVerifier
This is the key used to establish whether we should verify the audience.
verifyColumnType(Connection, String, String, int) - Static method in class org.intermine.sql.DatabaseUtil
 
verifyQuery() - Method in class org.intermine.pathquery.PathQuery
Verifies the contents of this query against the model, and for internal integrity.
VerifyTokenTask - Class in org.intermine.web.task
A task to check that a token can be verified.
VerifyTokenTask() - Constructor for class org.intermine.web.task.VerifyTokenTask
 
version - Variable in class org.intermine.pathquery.PathQueryHandler
 
version - Variable in class org.intermine.sql.Database
 
VERSION - Static variable in class org.intermine.webservice.client.core.Service
The version of this client library.
Version - Class in org.intermine.webservice.client.core
Simple class representing service version.
Version(int, int, int) - Constructor for class org.intermine.webservice.client.core.Version
Constructor.
VERSION_PARAMETER - Static variable in class org.intermine.webservice.server.query.QueryUploadService
The key for the version parameter
VERSION_PARAMETER - Static variable in class org.intermine.webservice.server.template.TemplateUploadService
The key for the version parameter
VersionService - Class in org.intermine.webservice.server
Service for returning the version of this service.
VersionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.VersionService
Constructor
VersionServlet - Class in org.intermine.webservice.server
Returns version of the deployed InterMine application.
VersionServlet() - Constructor for class org.intermine.webservice.server.VersionServlet
 
visible - Variable in class org.intermine.api.results.Column
 
visitLeft(A) - Method in class org.intermine.webservice.server.core.EitherVisitor
Override this to access the left hand side.
visitLeft(L) - Method in class org.intermine.webservice.server.core.TreeWalker
 
visitRight(B) - Method in class org.intermine.webservice.server.core.EitherVisitor
Override this to access the right hand side.
visitRight(DisjointRecursiveList<L>) - Method in class org.intermine.webservice.server.core.TreeWalker
 

W

waitForCurrentJobs() - Method in class org.intermine.sql.Database
Blocks until all the current pending jobs are finished.
wantsColumnHeaders() - Method in class org.intermine.webservice.server.WebService
Returns true if the request wants column headers as well as result rows
warning(SAXParseException) - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler
}
wasSuccessful() - Method in interface org.intermine.api.idresolution.Job
 
wasSuccessful() - Method in class org.intermine.api.idresolution.ResolutionJob
 
wasSuccessful() - Method in class org.intermine.api.idresolution.UpgradeJob
 
WeakReferenceHashMap<K,V> - Class in org.intermine.util
This is a Map implementation designed specifically for people intending to create a cache.
WeakReferenceHashMap(int, float) - Constructor for class org.intermine.util.WeakReferenceHashMap
Constructs a new, empty WeakReferenceHashMap with the given initial capacity and the given load factor.
WeakReferenceHashMap(int) - Constructor for class org.intermine.util.WeakReferenceHashMap
Constructs a new, empty WeakReferenceHashMap with the given initial capacity and the default load factor, which is 0.75.
WeakReferenceHashMap() - Constructor for class org.intermine.util.WeakReferenceHashMap
Constructs a new, empty WeakReferenceHashMap with the default initial capacity (16) and the default load factor (0.75).
WeakReferenceHashMap(String) - Constructor for class org.intermine.util.WeakReferenceHashMap
Constructs a new, empty WeakReferenceHashMap with the default initial capacity (16) and the default load factor (0.75), and a name.
WeakReferenceHashMap(Map<K, V>) - Constructor for class org.intermine.util.WeakReferenceHashMap
Constructs a new WeakReferenceHashMap with the same mappings as the specified Map.
WeakReferenceMap<K,V> - Class in org.intermine.util
This is a Map implementation designed specifically for people intending to create a cache.
WeakReferenceMap() - Constructor for class org.intermine.util.WeakReferenceMap
 
WEB_PROPERTIES - Static variable in class org.intermine.web.logic.Constants
ServletContext attribute used to store web.properties
WEB_SERVICE_VERSION - Static variable in class org.intermine.web.logic.Constants
Current version of the InterMine WebService.
WEB_STATE - Static variable in class org.intermine.web.logic.Constants
Session attribute used to store WebState object.
webConfig - Variable in class org.intermine.web.logic.bag.BagConverter
 
WebConfig - Class in org.intermine.web.logic.config
Configuration object for web site
WebConfig() - Constructor for class org.intermine.web.logic.config.WebConfig
 
WEBCONFIG - Static variable in class org.intermine.web.logic.Constants
ServletContext attribute used to store the WebConfig object for the Model.
webConfig - Variable in class org.intermine.web.logic.results.InlineResultsTable
 
WebJobInput - Class in org.intermine.web.logic.bag
 
WebJobInput(String, Collection<String>, BuildBagForm) - Constructor for class org.intermine.web.logic.bag.WebJobInput
Create a web-job.
webProperties - Variable in class org.intermine.api.LinkRedirectManager
 
webProperties - Variable in class org.intermine.webservice.server.WebService
The properties this mine was configured with
WebResults - Class in org.intermine.api.results
The web version of a Results object.
WebResults(InterMineAPI, PathQuery, Results, Map<String, QuerySelectable>, Map<String, BagQueryResult>) - Constructor for class org.intermine.api.results.WebResults
Create a new WebResults object.
WebResultsExecutor - Class in org.intermine.api.query
Executes a PathQuery and returns a WebResults object, to be used when multi-row style results are required.
WebResultsExecutor(InterMineAPI, Profile) - Constructor for class org.intermine.api.query.WebResultsExecutor
Constructor with necessary objects to generate an ObjectStore query from a PathQuery and execute it.
WebSearchable - Interface in org.intermine.api.search
An interface implemented by objects that we want to index with Lucene.
WebSearchableListController - Class in org.intermine.web.struts
Controller for webSearchableList.tile
WebSearchableListController() - Constructor for class org.intermine.web.struts.WebSearchableListController
 
WebSearchWatcher - Interface in org.intermine.api.search
The interface for describing objects that listen to WebSearchables for events.
WebService - Class in org.intermine.webservice.server
Base class for web services.
WebService(InterMineAPI) - Constructor for class org.intermine.webservice.server.WebService
Construct the web service with the InterMine API object that gives access to the core InterMine functionality.
WebserviceCodeGenAction - Class in org.intermine.web.struts
Action to handle the web service code generation.
WebserviceCodeGenAction() - Constructor for class org.intermine.web.struts.WebserviceCodeGenAction
 
WebserviceCodeGenerator - Interface in org.intermine.api.query.codegen
Interface for web service code generation.
WebserviceCodeGenInfo - Class in org.intermine.api.query.codegen
Class to represent the information used to generate web service source code.
WebserviceCodeGenInfo(PathQuery, String, String, String, boolean, Profile) - Constructor for class org.intermine.api.query.codegen.WebserviceCodeGenInfo
Constructor.
WebserviceCodeGenInfo(PathQuery, String, String, String, boolean, Profile, String) - Constructor for class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
WebServiceConstants - Class in org.intermine.webservice.server
 
WebServiceInput - Class in org.intermine.webservice.server
Base class for input classes used with web services.
WebServiceInput() - Constructor for class org.intermine.webservice.server.WebServiceInput
 
WebserviceJavaCodeGenerator - Class in org.intermine.api.query.codegen
This Class generates Java source code of web service client for path query and template query.
WebserviceJavaCodeGenerator() - Constructor for class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
WebserviceJavaScriptCodeGenerator - Class in org.intermine.api.query.codegen
A Class for generating JavaScript that would run a given query.
WebserviceJavaScriptCodeGenerator() - Constructor for class org.intermine.api.query.codegen.WebserviceJavaScriptCodeGenerator
 
WebservicePerlCodeGenerator - Class in org.intermine.api.query.codegen
This Class generates Perl source code of web service client for path query and template query.
WebservicePerlCodeGenerator() - Constructor for class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
WebservicePythonCodeGenerator - Class in org.intermine.api.query.codegen
Class for generating Python code to run a query, using the intermine python library.
WebservicePythonCodeGenerator() - Constructor for class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
 
WebServiceRequestParser - Class in org.intermine.webservice.server
Base request parser that is used by advanced web service parsers.
WebServiceRequestParser() - Constructor for class org.intermine.webservice.server.WebServiceRequestParser
 
WebserviceRubyCodeGenerator - Class in org.intermine.api.query.codegen
 
WebserviceRubyCodeGenerator() - Constructor for class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
WebServiceServlet - Class in org.intermine.webservice.server.core
A servlet which can be easily configured to define how to route requests, using standard RESTful semantics.
WebServiceServlet() - Constructor for class org.intermine.webservice.server.core.WebServiceServlet
Constructor
WebServiceServlet.Method - Enum in org.intermine.webservice.server.core
 
WebState - Class in org.intermine.web.logic.results
This class saves things related to the state of web GUI.
WebState() - Constructor for class org.intermine.web.logic.results.WebState
 
WebTable - Interface in org.intermine.api.results
A List that can understand ResultElement objects.
WebUtil - Class in org.intermine.web.logic
Utility methods for the web package.
WebUtil.HeadResource - Class in org.intermine.web.logic
A bean encapsulating a resource (js or css).
welcome(String) - Method in class org.intermine.util.Emailer
Welcome a user to the system.
welcome(String, Properties) - Static method in class org.intermine.util.MailUtils
Send a welcoming email to an email address
welcome(String) - Method in class org.intermine.web.context.NullMailer
 
where - Variable in class org.intermine.sql.query.Query
 
whereHavingSafe(Object, Query) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Returns an array containing two boolean values.
whichColumn - Variable in class org.intermine.bio.dataconversion.TreefamConverter.GeneHolder
 
WHITELIST - Static variable in class org.intermine.webservice.server.JWTVerifier
This is where we get the list of aliases from if the strategy is WHITELIST
WhoAmIService - Class in org.intermine.webservice.server.user
Class for retrieving information about the currently authenticated user.
WhoAmIService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.WhoAmIService
Constructor
WhoAmIServlet - Class in org.intermine.webservice.server.user
 
WhoAmIServlet() - Constructor for class org.intermine.webservice.server.user.WhoAmIServlet
 
Widget - Class in org.intermine.web.logic.widget
A representation of a query using a list tool.
Widget(WidgetConfig) - Constructor for class org.intermine.web.logic.widget.Widget
The constructor
Widget - Class in org.intermine.webservice.client.widget
A representation of a list analysis widget, containing the metadata necessary to describe its usage and to choose how and whether to display its results.
Widget(String, String, String, String, String, Collection<String>, Collection<String>, String, String) - Constructor for class org.intermine.webservice.client.widget.Widget
Constructor.
WidgetConfig - Class in org.intermine.web.logic.widget.config
Class representing a Widget Configuration
WidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.WidgetConfig
 
WidgetConfigUtil - Class in org.intermine.web.logic.widget.config
Utilities for handling the widget configuration
WidgetForm - Class in org.intermine.web.struts
 
WidgetForm() - Constructor for class org.intermine.web.struts.WidgetForm
Constructor
WidgetHelper - Interface in org.intermine.web.logic.widget
An Interface for widget Utils
widgetId - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
WidgetLdr - Class in org.intermine.web.logic.widget
The class that performs the actual queries for widgets.
WidgetLdr(InterMineBag, ObjectStore, String, WidgetConfig) - Constructor for class org.intermine.web.logic.widget.WidgetLdr
 
WidgetOptions - Interface in org.intermine.web.logic.widget
The type of options a widget would expect to receive.
WidgetProcessor - Interface in org.intermine.webservice.server.widget
 
WidgetProcessorImpl - Class in org.intermine.webservice.server.widget
A base class for Widget Processors
WidgetProcessorImpl() - Constructor for class org.intermine.webservice.server.widget.WidgetProcessorImpl
 
WidgetProcessorImpl.WidgetType - Enum in org.intermine.webservice.server.widget
Of widget types there are several:
WidgetResultProcessor - Interface in org.intermine.webservice.server.widget
Interfaces for classes that are able to process the results that widgets return.
WidgetService - Class in org.intermine.webservice.client.services
A class for managing widget operations.
WidgetService(String, String) - Constructor for class org.intermine.webservice.client.services.WidgetService
Use ServiceFactory instead of constructor for creating this service .
WidgetService - Class in org.intermine.webservice.server.widget
 
WidgetService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.WidgetService
Construct the webservice controller.
WidgetsRequestParser - Class in org.intermine.webservice.server.widget
Request processor for WidgetsService that process request, validates it and returns parsed input as a parameter object.
WidgetsRequestParser() - Constructor for class org.intermine.webservice.server.widget.WidgetsRequestParser
ListsRequestProcessor constructor.
WidgetsServiceInput - Class in org.intermine.webservice.server.widget
WidgetsServiceInput is parameter object representing parameters for the WidgetsService web service.
WidgetsServiceInput() - Constructor for class org.intermine.webservice.server.widget.WidgetsServiceInput
 
WidgetsServiceInput.Builder - Class in org.intermine.webservice.server.widget
Class to build Inputs for the Widget Service.
WidgetsServiceInput.Builder() - Constructor for class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
 
WidgetsServlet - Class in org.intermine.webservice.server.widget
Servlet running WidgetsService.
WidgetsServlet() - Constructor for class org.intermine.webservice.server.widget.WidgetsServlet
 
width - Variable in class org.intermine.sql.query.ExplainResult
 
WIDTH_BUCKET - Static variable in class org.intermine.objectstore.query.QueryFunction
Get the bucket this value would be assigned in an equal-depth histogram.
WidthBucketFunction - Class in org.intermine.objectstore.query
Representation of a call to the Postgresql WIDTH_BUCKET function.
WidthBucketFunction(QueryEvaluable, QueryEvaluable, QueryEvaluable, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.WidthBucketFunction
Constructor.
WILDCARD - Static variable in class org.intermine.api.bag.BagQueryResult
Key of the Map returned by getIssues() when the object found by querying with a wildcard.
wildcardSqlToUser(String) - Static method in class org.intermine.metadata.Util
Deprecated.
I don't think this is used anymore?
wildcardUserToSql(String) - Static method in class org.intermine.metadata.Util
Turn a user supplied wildcard expression with * into an SQL LIKE/NOT LIKE expression with %'s and other special characters.
WINDOWS_SEPARATOR - Static variable in interface org.intermine.web.logic.export.Exporter
Windows line separator CR+LF
WITHIN - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument lie entirely within the second.
withinRange(int) - Method in class org.intermine.webservice.server.core.Page
 
WORM_LINK - Static variable in class org.intermine.bio.web.export.GFF3Exporter
for the gff header, link to taxomony
WormBaseIdResolverFactory - Class in org.intermine.bio.dataconversion
Create an IdResolver for Worm genes by querying tables in a WormBase chado database.
WormBaseIdResolverFactory() - Constructor for class org.intermine.bio.dataconversion.WormBaseIdResolverFactory
constructor
WormBaseIdResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.WormBaseIdResolverFactory
Construct with SO term of the feature type to read from chado database.
WormBaseProcessor - Class in org.intermine.bio.dataconversion
A converter for chado that handles WormBase specific configuration.
WormBaseProcessor(ChadoDBConverter) - Constructor for class org.intermine.bio.dataconversion.WormBaseProcessor
Create a new WormBaseChadoDBConverter.
wrapLines(String, int, int) - Static method in class org.intermine.metadata.StringUtil
Wraps the given String into several lines and ultimately truncates it with an ellipsis.
wrapLines(String, int, int, int) - Static method in class org.intermine.metadata.StringUtil
Wraps the given String into several lines and ultimately truncates it with an ellipsis.
write(int) - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream
 
write(byte[], int, int) - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream
 
write(char[], int, int) - Method in class org.intermine.sql.logging.DatabaseWriter
Write a portion of an array to the database
write(Connection, Map<String, ? extends Table>, Set<String>) - Method in interface org.intermine.sql.writebatch.BatchWriter
Performs all the processing for flushing a few tables to the connection, and returns a List of jobs to do the actual flushing.
write(Connection, Map<String, ? extends Table>, Set<String>) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Performs all the processing for flushing a few tables to the connection, and returns a List of jobs to do the actual flushing.
write(int) - Method in class org.intermine.util.SensibleByteArrayOutputStream
write(byte[], int, int) - Method in class org.intermine.util.SensibleByteArrayOutputStream
write(XMLStreamWriter, Profile, ObjectStore) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
Write template-queries and tags elements.
write(Iterator<List<ResultElement>>, Output) - Method in class org.intermine.webservice.server.core.ResultProcessor
Writes results to output.
write(Iterator<List<ResultElement>>, Output) - Method in class org.intermine.webservice.server.output.JSONResultProcessor
 
writeCount(int, Output) - Method in class org.intermine.webservice.server.core.CountProcessor
Write the count to the output.
writeLargeUTF(String) - Method in class org.intermine.sql.writebatch.PostgresDataOutputStream
Writes the given String to the stream in modified UTF-8 format, following its length in bytes as a four-byte integer.
writeLargeUTF(StringConstructor) - Method in class org.intermine.sql.writebatch.PostgresDataOutputStream
Writes the given StringConstructor to the stream in modified UTF-8 format, following its length in bytes as a four-byte integer.
writeLargeUTF(Collection<String>) - Method in class org.intermine.sql.writebatch.PostgresDataOutputStream
Writes the given Collection of Strings to the stream in modified UTF-8 format, following its length in bytes as a four-byte integer.
writePendingClobs(Connection, Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Writes the contents of any pending Clobs to the database, and replaces them in the objects with a real ClobAccess object.
writers - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
writeToFile(File) - Method in class org.intermine.bio.dataconversion.IdResolver
Write IdResolver contents to a flat file
writtenObjects - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
This is a list of the objects in the destination database that we have written to as a non-skeleton.

X

xml - Variable in class org.intermine.web.struts.ImportXMLForm
 
xml(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoadQueryAction
Load a query from path query XML passed as a request parameter.
XmlBinding - Class in org.intermine.util
Represents an XML mapping - performs XML (un)marshalling of objects/Full Data XML
XmlBinding(Model) - Constructor for class org.intermine.util.XmlBinding
Constructor
XmlDataLoader - Class in org.intermine.dataloader
Provides a method for unmarshalling XML given source into java business objects then calls store on each.
XmlDataLoader(IntegrationWriter) - Constructor for class org.intermine.dataloader.XmlDataLoader
 
XmlDataLoaderTask - Class in org.intermine.dataloader
Uses an IntegrationWriter to load data from XML format
XmlDataLoaderTask() - Constructor for class org.intermine.dataloader.XmlDataLoaderTask
 
xmlFile - Variable in class org.intermine.task.XPathSelect
 
XMLFormatter - Class in org.intermine.webservice.server.output
Formats data to XML format.
XMLFormatter() - Constructor for class org.intermine.webservice.server.output.XMLFormatter
 
XmlHelper - Class in org.intermine.xml
Static methods to assist parsing and rendering of XML.
xmlRes - Variable in class org.intermine.dataloader.XmlDataLoaderTask
 
xmlRes - Variable in class org.intermine.task.FullXmlConverterTask
 
XMLTableResult - Class in org.intermine.webservice.client.results
A utility class for parsing tab separated values in the results.
XMLTableResult(HttpConnection) - Constructor for class org.intermine.webservice.client.results.XMLTableResult
Constructor.
XMLTableResult(String) - Constructor for class org.intermine.webservice.client.results.XMLTableResult
Constructor.
XMLTableResult(BufferedReader) - Constructor for class org.intermine.webservice.client.results.XMLTableResult
Constructor with a reader.
xmlToTemplateMap(String, Map<String, InterMineBag>, int) - Static method in class org.intermine.api.template.TemplateHelper
Parse templates in XML format and return a map from template name to TemplateQuery.
XmlUtil - Class in org.intermine.util
General-purpose methods for manipulating URIs and XML schema types
XMLValidator - Class in org.intermine.webservice.server.query.result
XMLValidator is class that validates xml string according an XML Schema at specified url.
XMLValidator() - Constructor for class org.intermine.webservice.server.query.result.XMLValidator
 
XMLValidatorErrorHandler - Class in org.intermine.webservice.server.query.result
 
XMLValidatorErrorHandler() - Constructor for class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler
 
XMLWidgetProcessor - Class in org.intermine.webservice.server.widget
A processor for handling requests for widget metadata.
XPathSelect - Class in org.intermine.task
An ANT Task to retrieve a string into a property from an XML file using an XPath expression.
XPathSelect() - Constructor for class org.intermine.task.XPathSelect
 
XRef - Class in org.intermine.bio.web
This is a bean to store cross-reference data This class is half finished, more fields may be added
XRef() - Constructor for class org.intermine.bio.web.XRef
 
xrefs - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord
 
xrefs - Variable in class org.intermine.bio.dataconversion.OboConverter
 

Y

youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryCast
Allows a caller to suggest to this object that it holds a value of a certain type.
youAreType(Class<?>) - Method in interface org.intermine.objectstore.query.QueryEvaluable
Allows a caller to suggest to this object that it holds a value of a certain type.
youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryExpression
Allows a caller to suggest to this object that it holds a value of a certain type.
youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryField
Allows a caller to suggest to this object that it holds a value of a certain type.
youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryForeignKey
Allows a caller to suggest to this object that it holds a value of a certain type.
youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryFunction
Allows a caller to suggest to this object that it holds a value of a certain type.
youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryValue
Allows a caller to suggest to this object that it holds a value of a certain type.

Z

ZERO - Static variable in class org.intermine.web.logic.widget.ErrorCorrection
 
ZERO_PROFILE_VERSION - Static variable in class org.intermine.api.xml.ProfileManagerBinding
Default version of profile if it is not specified.
ZfinIdentifiersResolverFactory - Class in org.intermine.bio.dataconversion
ID resolver for ZFIN genes.
ZfinIdentifiersResolverFactory() - Constructor for class org.intermine.bio.dataconversion.ZfinIdentifiersResolverFactory
Construct without SO term of the feature type.
ZfinIdentifiersResolverFactory(String) - Constructor for class org.intermine.bio.dataconversion.ZfinIdentifiersResolverFactory
Construct with SO term of the feature type.
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z